bluuebunny/crossref_metadata_2025_split huggingface dataset:
Robust discrimination between closely related species of salmon based on DNA fragments
Authors: Ellisor Debra , Gregg Mary , Folz Angela , Possolo Antonio 
Published: January 2025

Abstract
Closely related species of Salmonidae, including Pacific and Atlantic salmon, can be distinguished from one another based on nucleotide sequences from the cytochrome c oxidase sub-unit 1 mitochondrial gene (COI), using ensembles of fragments aligned to genetic barcodes that serve as digital proxies for the relevant species. This is accomplished by exploiting both the nucleotide sequences and their quality scores recorded in a FASTQ file obtained via Next Generation (NextGen) Sequencing of mitochondrial DNA extracted from Coho salmon caught with hook and line in the Gulf of Alaska. The alignment is done using MUSCLE (Muscle 5.2) [1], applied to multiple versions of each fragment perturbed according to the nucleobase identification error probabilities underlying the quality scores. The Damerau-Levenshtein distance was used to determine the genetic barcode of the candidate species that is closest to each aligned, perturbed fragment. The “votes” that the sampled fragments cast for the different candidate species are then pooled and converted into identification probabilities, using weights determined by the entropy of the fragment-specific identification probability distributions. This novel approach to quantify the uncertainty associated with measurements made using NextGen Sequencing can be applied to discriminate closely related species, hence to value-assignment for reference materials supporting determinations of the authenticity of seafood, for example, NIST Reference Materials 8256 and 8257 (Coho salmon) [2].
Regularity of Conjugacies of Linearizable Generalized Interval Exchange Transformations
Authors: Ghazouani Selim , Ulcigrai Corinna 
Published: January 2025

Abstract
We consider generalized interval exchange transformations (GIETs) of

$$d\ge 2$$

d
≥
2

intervals which are linearizable, i.e. differentiably conjugated to standard interval exchange maps (IETs) via a diffeomorphism h of [0, 1] and study the regularity of the conjugacy h. Using a renormalization operator obtained accelerating Rauzy–Veech induction, we show that, under a full measure condition on the IET obtained by linearization, if the orbit of the GIET under renormalization converges exponentially fast in a

$${\mathcal {C}}^2$$

C

2

distance to the subspace of IETs, there exists an exponent

$$0<\alpha <1$$

0
<
α
<
1

such that h is

$${\mathcal {C}}^{1+\alpha }$$

C

1
+
α

. Combined with the results proved by the authors in [4], this implies in particular the following improvement of the rigidity result in genus two proved in [4] (from

$${\mathcal {C}}^1$$

C

1

to

$${\mathcal {C}}^{1+\alpha }$$

C

1
+
α

rigidity): for almost every irreducible IET

$$T_0 $$

T
0

with

$$d=4$$

d
=
4

or

$$d=5$$

d
=
5

, for any GIET which is topologically conjugate to

$$T_0$$

T
0

via a homeomorphism h and has vanishing boundary, the topological conjugacy h is actually a

$${\mathcal {C}}^{1+\alpha }$$

C

1
+
α

diffeomorphism, i.e. a diffeomorphism h with derivative Dh which is

$$\alpha $$

α

-Hölder continuous.
Are we underestimating pathological fracture risk in malignant bone lesions of the proximal humerus?
Authors: Weschenfelder Wolfram , Weschenfelder Friederike , Spiegel Christian , Schrenk Karin Gabriela , Hofmann Gunther Olaf 
Published: January 2025

Abstract

Objective
This study is aimed at evaluating the distribution of metastatic bone disease (MBD), with a particular focus on the humerus, and its association with pathological fractures. Factors for contributing to the underestimation of fracture risk were assessed, including their impact on surgical management.

Materials and methods
We retrospectively reviewed patient records of patients undergoing surgical treatment for MBD at our institution between 2005 and 2023. The analysis included factors such as medical history, tumour type, metastatic status, surgical method, lesion location, and imaging. The images of local and staging studies (CT chest/abdomen/pelvis, CT skeleton body, bone scan, PET/CT) were reviewed by two observers. Group comparisons were made based on lesion localisation.

Results
The two most affected bone regions were the proximal femur (39.4%), followed by the proximal humerus (13.5%). Lesions of the proximal humerus were significantly more likely to be associated with pathological fractures compared to those of the proximal femur and other localisations (p < 0.01). Identified potential causes include less frequent depiction of the proximal humerus during staging (29% vs. 79% and 51%; p < 0.01) and overall lower Mirel’s scores despite the number of fractures (8 vs. 10 and 9; p < 0.01).

Conclusion
Metastatic bone disease (MBD) in the proximal humerus is less frequently captured in current staging imaging, particularly CT chest/abdomen/pelvis. Additionally, fracture prediction using Mirel’s scoring often underestimates the actual risk. Staging investigations should include this region more comprehensively, and even when correctly imaged, better tools are needed to evaluate bone metastases effectively.
The global prevalence of interstitial lung disease in patients with rheumatoid arthritis: a systematic review and meta-analysis
Authors: Prasanna Hari , Inderjeeth Charles A. , Nossent Johannes C. , Almutairi Khalid B. 
Published: January 2025

Abstract
This study aims to review the literature and estimate the global pooled prevalence of interstitial lung disease among patients with rheumatoid arthritis (RA-ILD). The influence of risk factors like geography, socioeconomic status, smoking and DMARD use will be explored. A systematic review was performed according to the PRISMA and JBI guidelines. Studies published between January 1980 and February 2024 were sourced from 7 electronic databases and screened for eligibility. A random-effects meta-analysis model was used to produce pooled prevalences and the potential between-study heterogeneity was identified using sensitivity, subgroup, meta-regression and correlation analyses. 33 studies were included in this meta-analysis containing 14,281 RA patients. The global pooled prevalence of RA-ILD was 21.38% (CI: 0.1542–0.2886), with a high heterogeneity (I2) of 98%. The prevalence of usual interstitial pneumonia and non-specific interstitial pneumonia among RA patients were 11.01% and 6.86% respectively. Africa had the highest RA-ILD prevalence with an imprecise estimate of 38.15% (95% Confidence Interval [CI]: 2.29–94.2) and Europe had the lowest prevalence of 10.15% (CI: 2.86–30.23). Other risk factors associated with a higher prevalence of RA-ILD included living in low-income countries, smoking and DMARD use. The biggest limitation of this study is the high heterogeneity of results and underrepresentation of Oceania and low-income countries. This study has clarified the global prevalence of RA-ILD. The risk factors identified in this study can aid clinicians in identifying high-risk populations and highlight the need for screening these populations. Smoking cessation should also be encouraged.
Tunica vaginalis or dartos as second layer coverage for distal and mid-shaft penile hypospadias, quo vadis?
Authors: Ramez Mohamed , Hashem Abdelwahab , Bazeed Mahmoud , Dawaba Mohamed S. , Helmy Tamer E. 
Published: January 2025

Abstract

Purpose
To compare between the dartos and tunica vaginalis flaps as covering layers in denovo distal or mid-shaft penile hypospadias underwent tubularized incised plate (TIP) repair.

Methods
This is a single-center, randomized trial was for denovo distal or mid-shaft penile hypospadias. Children with history of orchiectomy, orchiopexy and inguinal hernia repair were excluded. Eighty-eight patients were divided into two groups: the first used dartos flap (DF), while the second used tunica vaginalis flap (TVF). The primary outcome was to assess the incidence of urethrocutaneous fistula. The secondary outcome was to assess cosmetic outcome using paediatric penile perception score (PPPS) and hypospadias objective scoring evaluation (HOSE).

Results
Baseline demographic and clinical characteristics showed no statistically significant. Median operative time (IQR) was 100 (90, 120) and 145 (140, 150) minutes in in DF and TVF Groups, respectively (p < 0.001). Urethrocutaneous Fistula was detected in 9 (20.9%) in DF group and 2 (4.9%) in TVF group (p 0.029). Meatal stenosis occurred in 3 (7%) in DF group and 2 (4.9%) in TVF group. Penile torque was diagnosed in one (2.4%) in TVF group. There was no significant difference in total PPPS score (p = 0.076), however, there was a significant difference in total HOSE score in the favour to TVF group (p = 0.024). At 12 months, testicular ascent occurred in 0% and 3 (7.3%) in DF and TVF groups, respectively (p = 0.071).

Conclusion
Compared to dartos flap, tunica vaginalis flap significantly helps in reduction of fistula rate. However, it has significant more operative time.
Comparison of failure rates between full-barium and striped barium distal shunt catheters: a matched case–control study
Authors: Rahm Sage P. , Laskay Nicholas M. B. , McClugage Samuel G. , Jackson Joshua D. , Arynchyna-Smith Anastasia , Rozzelle Curtis J. , Rocque Brandon G. 
Published: January 2025

Abstract

Purpose
We hypothesize that distal shunt catheters fully impregnated with barium are more prone to failure compared to distal catheters with only a barium stripe. We sought to evaluate this distinction using a matched case–control study.

Methods
Patient records over an 8-year period were queried for distal shunt revisions for fracture or disconnection (cases). A control group of patients with confirmed functioning distal catheters was queried from the same period and matched based on patient age at exploration/revision. Data were collected via chart review, including demographics, hydrocephalus etiology, distal catheter type, and patient age at revision. Independent T-test, chi-squared, and binomial logistic regression analyses were performed.

Results
There were 194 patients included in the study: 97 patients with distal shunt revision and 97 controls with a functional distal shunt system. The mean patient age at distal catheter revision was 12.87 ± 4.59 years, and the mean patient age of the control group was 12.81 ± 4.59 years. The most common etiology was premature intraventricular hemorrhage (32%). Of the distal failures, 41.2% had fully impregnated barium catheters, while 58.8% had striped barium catheters. Of the control group, 76/97 (78%) patients had barium-striped distal shunt catheters and 21/97 (22%) had fully impregnated catheters. Logistic regression analysis showed that fully impregnated catheters were more likely than striped barium to fail, p = 0.004 (OR = 2.54, 95% CI 1.35–4.77).

Conclusion
In a matched case–control format, odds of failure of fully impregnated distal catheters were 2.54 greater than striped barium catheters.
The tumor immune microenvironment in primary cutaneous melanoma
Authors: Zilberg Catherine , Ferguson Angela L. , Lyons J. Guy , Gupta Ruta , Damian Diona L. 
Published: January 2025

Abstract
Melanoma is an immunogenic tumor. The melanoma tumor immune microenvironment (TIME) is made up of a heterogenous mix of both immune and non-immune cells as well as a multitude of signaling molecules. The interactions between tumor cells, immune cells and signaling molecules affect tumor progression and therapeutic responses. Understanding the composition and function of the TIME in primary cutaneous melanoma is useful for prognostication and therapeutic decisions. This review provides an overview of the components of the TIME in primary cutaneous melanoma, and their influence on clinical outcomes.
Surgeon’s imposter syndrome: a systematic review
Authors: El Boghdady Michael , Ewalds-Kvist Béatrice 
Published: January 2025

Abstract

Introduction
Imposter syndrome (IS) refers to the psychological experience of imagining that one’s achievements do not originate from one’s own authentic competence. Surgeons are constantly faced with life-threatening decisions and can easily feel inadequate or insecure despite their years of training and experience. Imposter syndrome can distress surgeons at all career stages and has profound psychological and professional consequences. We aimed to review imposter syndrome in surgeons.

Methods
A systematic search was performed in compliance with The PRISMA checklist. Search was performed in the PubMed and ScienceDirect databases. We included articles about IS in surgeons. We excluded narrative articles, commentaries and studies involving medical students or other specialties. Citations were quality assessed by MERSQI and evidence graded (GRADE). Risk of bias was assessed among the included citations.

Results
The search revealed 695 citations, from which a final list of 12 was compiled after applying the inclusion and exclusion criteria. Participants included trainees and consultant surgeons across various surgical specialties. The following research questions were answered: Are surgeons with IS predisposed to mental or physical challenges? Do surgeons experience gender differences in IS? Can the feeling of IS be reduced?

Conclusion
There is a high prevalence of imposter syndrome among surgeons. Surgeons with IS are predisposed to experience mental or physical challenges. Female surgeons experience IS more frequently than their male counterparts. Feelings of IS can decline with increasing age but also with other included methods. Risks and multiple preventative measures were explored. The key to reducing IS is to train oneself to discern fact from fiction, thereby undermining distorted thoughts that perpetuate feelings of being an imposter.
The treatment of acute traumatic aortic injuries with TEVAR: a retrospective analysis of 19 cases in a level-1 trauma center
Authors: Liese-Landolt F. , Pape H.-C. , Jukema G. N. 
Published: January 2025

Abstract

Introduction
Blunt traumatic aortic injury (TAI) is a critical condition and a leading cause of mortality in trauma patients, often resulting from high-speed accidents. Thoracic endovascular aortic repair (TEVAR) has developed into the preferred therapeutic approach due to its minimally invasive nature and promising outcomes. This study evaluates the safety and efficacy of TEVAR for managing TAI over a 10-year period at a Level-1 trauma center.

Methods
A retrospective analysis was conducted on 19 patients with acute TAI treated with TEVAR between 2012 and 2022 at the University Hospital Zurich. Data were collected from digital records and analyzed according to the Fillinger TEVAR reporting framework. Outcomes included technical success, perioperative complications, and long-term graft durability.

Results
The cohort had a mean age of 39 years and included patients with severe polytrauma. Technical success was achieved in 95% of cases, with no intraoperative deaths or need for open surgical conversion. Perioperative complications were minimal, and the reintervention rate was 5.3%. This study evaluates 10 years of clinical experience managing TAI with TEVAR. Long-term follow-up, with a median duration of 29 months, revealed no graft-related complications or secondary interventions. Imaging confirmed sustained graft integrity, and clinical outcomes were favorable.

Conclusion
TEVAR is a reliable and effective treatment for traumatic aortic injuries, offering excellent technical success rates and minimal perioperative and long-term complications. This study highlights TEVAR’s advantages in managing polytrauma patients and its role as a minimally invasive alternative to open surgery. Additionally, the findings emphasize the need for comprehensive long-term follow-up protocols. Future research should aim to address challenges related to device durability and the integration of advanced imaging techniques to further enhance patient outcomes and broaden the applicability of TEVAR in trauma care.
Estimating simplet counts via sampling
Authors: Kim Hyunju , Moon Heechan , Bu Fanchen , Ko Jihoon , Shin Kijung 
Published: January 2025

Abstract
Simplicial complexes are higher-order combinatorial structures which have been used to represent real-world complex systems. In this paper, we focus on the local patterns in simplicial complexes called simplets, a generalization of graphlets. We study the problem of counting simplets of a given size in a given simplicial complex. For this problem, we extend a sampling algorithm based on color coding, from graphs to simplicial complexes, with essential technical novelty. We theoretically analyze our proposed algorithm named SC3, showing its correctness, unbiasedness, convergence, and time/space complexity. Through extensive experiments on sixteen real-world datasets, we show the superiority of SC3 in terms of accuracy, speed, and scalability, compared to the baseline methods. We use the counts given by SC3 for simplicial complex analysis, especially for characterization, which is further used for simplicial complex clustering, where SC3 shows a strong ability of characterization with domain-based similarity. Additionally, we explore a variant of simplet counting (specifically, estimating the relative counts of simplets) under realistic scenarios where the entire simplicial complex is not provided at once but can only be partially accessed, for instance, through a limited number of API calls. For such scenarios, we propose a random-walk-based sampling algorithm, SCRW, and analyze its theoretical properties. In our experiments, SCRW requires, on average,

$$16.5\times $$

16.5
×

less memory than SC3, while the speed-accuracy trade-offs provided by the two methods are comparable.
Reciprocal relationships between adolescent mental health difficulties and alcohol consumption
Authors: Kiri Janet , Hall James , Cortese Samuele , Brandt Valerie 
Published: January 2025

Abstract
The directionality of the relationship between adolescent alcohol consumption and mental health difficulties remains poorly understood. This study investigates the longitudinal relationship between alcohol use frequency, internalizing and externalizing symptoms from the ages of 11 to 17. We conducted a random-intercept cross-lagged panel model across three timepoints (ages: 11yrs, 14yrs, 17yrs; 50.4% female) in the Millennium Cohort Study (N = 10,647). Survey weights were used to account for attrition. At each timepoint, past month alcohol use frequency was self-reported, parents and cohort members reported internalizing/externalizing symptoms using the Strengths and Difficulties Questionnaire. We controlled for alcohol expectancies, sex, and four cumulative risk indices (perinatal risk, early childhood adverse parenting, longitudinal parent-level risk occurrence, and persistent household socioeconomic deprivation). More frequent past month alcohol use at age 11 predicted increased internalizing symptoms at age 14 (β = 0.06; p =.01). More frequent past month alcohol use at age 14 predicted increased externalizing symptoms at age 17 (β = 0.11; p <.001). Increased internalizing symptoms consistently predicted reduced alcohol use at the next timepoint throughout the study period (11 years: β= -0.04; p =.03; 14 years: β= -0.09; p <.001). Increased externalizing symptoms at age 11 predicted increased alcohol consumption at age 14 (β = 0.06; p =.004). Frequent adolescent alcohol consumption represents a significant risk for subsequent mental health difficulties. Externalizing symptoms and alcohol use frequency appear to exacerbate one another. Internalizing symptoms may reduce the risk of frequent alcohol consumption. Incorporating routine alcohol screening into adolescent mental health treatment settings could reduce the risk of comorbid externalizing and alcohol use disorders.
Fecal metabolomic analysis of the role of gut microbiota and short-chain fatty acids in the therapeutic mechanism of Timosaponin AIII in Sjögren’s syndrome
Authors: Pang Fengtao , Jiang Quan , Tang Xiaopo , Li Kesong 
Published: January 2025

Abstract

Introduction/objectives
Sjogren’s syndrome (SS) is a chronic inflammatory and difficult-to-treat autoimmune disease. Timosaponin AIII (TAIII), a plant-derived steroidal saponin, effectively inhibits cell proliferation, induces apoptosis, and exhibits anti-inflammatory properties. This study explored the mechanisms of action of TAIII in SS treatment by studying gut microbiota and short-chain fatty acids (SCFAs) using fecal metabolomics.

Methods
The model group used non-obese diabetic (NOD) mice. The treatment group was classified into TAIII and hydroxychloroquine groups. The gut microbiota, SCFAs, and metabolites were analyzed using 16S rRNA sequencing, gas chromatography–mass spectrometry analysis, and liquid chromatography–mass spectrometry, respectively.

Results
TAIII effectively alleviated dry mouth in NOD mice, slowed the progression of salivary gland tissue injury, reduced inflammatory factor expression, and increased the levels of aquaporins 1 and 5. TAIII regulated SCFA content and tryptophan metabolism by altering the abundance of the Rikenellaceae_RC9_gut_group, thereby reducing the inflammatory response. TAIII can improve imbalances in the gut microbiota and the metabolic levels of related SCFAs and tryptophan, thereby reducing the level of inflammation.

Conclusion
The significant differences observed in the abundance of the Rikenellaceae_RC9_gut_group between the treatment and control groups indicated the potential relationship between bacteria and metabolites in SS.

Key Points• The safe and effective treatment of SS with traditional Chinese medicine• Multi-means study on intestinal flora, short-chain fatty acids, and metabonomics