bluuebunny/crossref_metadata_2025_split huggingface dataset:
Relation of JAK2 V617F allele burden and coronary calcium score in patients with essential thrombocythemia
Authors: Drofenik Ajda , Blinc Ales , Bozic Mijovski Mojca , Pajic Tadej , Vrtovec Matjaz , Sever Matjaz 
Published: October 2024

Abstract

Background

JAK2 V617F (JAK2) mutation is associated with clonal hemopoiesis in myeloproliferative neoplasms as well as with faster progression of cardiovascular diseases. Little is known about the relationship between allele burden and the degree of atherosclerotic alteration of coronary vasculature. We previously reported that carotid artery stiffness progressed faster in patients with JAK2 positive essential thromocythemia (ET) patients. After a four-year follow-up we investigated whether mutation burden of a JAK2 allele correlates with a higher coronary calcium score.

Patients and methods
Thirty-six patients with JAK2 positive ET and 38 healthy matched control subjects were examined twice within four years. At each visit clinical baseline characteristics and laboratory testing were performed, JAK2 mutation burden was determined, and coronary calcium was measured.

Results

JAK2 allele burden decreased in 19 patients, did not change in 5 patients, and increased in 4 patients. The coronary calcium Agatston score increased slightly in both groups. Overall, there was no correlation between JAK2 allele burden and calcium burden of coronary arteries. However, in patients with the JAK2 mutation burden increase, the coronary calcium score increased as well.

Conclusions
The average JAK2 allele burden decreased in our patients with high-risk ET during the four-year period. However, in the small subgroup whose JAK2 mutation burden increased the Agatston coronary calcium score increased as well. This finding, which should be interpreted with caution and validated in a larger group, is in line with emerging evidence that JAK2 mutation accelerates atherosclerosis and can be regarded as a non-classical risk factor for cardiovascular disease.
Analysis of early diagnostic pathway for prostate cancer in Slovenia
Authors: Kokot Mateja Kokalj , Mirosevic Spela , Bric Nika , Petek Davorina 
Published: October 2024

Abstract

Background
Prostate cancer (PCa) is a prevalent male malignancy globally. Prolonged diagnostic intervals are associated with poorer outcomes, emphasizing the need to optimize this process. This study aimed to evaluate the doctor and primary care interval, research their impact on patient survival and explore opportunities to improve PCa diagnostic pathway in primary care.

Patients and methods
A retrospective cohort study using cancer patients' anonymised primary care data and data of the Slovenian Cancer Registry.

Results
The study found that the doctor interval had a median duration of 0 days (interquartile range ([IQR] 0–6) and primary care interval a median duration of 5 days (IQR 0–58). Longer intervals were observed in patients with more than two comorbidities, where general practitioners didn't have access to laboratory diagnostic tests within their primary health care centre and when patients first presented with symptoms (reported symptoms at first presentation: dysuria, lower urinary tract symptoms [LUTS], abdominal pain). The analysis also revealed a statistically significant association between lower 5-year survival rate and the accessibility of laboratory and ultrasound diagnostics in primary healthcare centres and a shorter 5-year survival of symptomatic patients in comparison to patients who were identified by elevated levels of prostate specific antigen (PSA).

Conclusions
This study shows that treating suspected PCa in primary care has a significant impact on 5-year survival. Several factors contribute to better survival, including easy access to laboratory and abdominal ultrasound in primary care centres. The study highlights the complex array of factors shaping PCa diagnosis, beyond individual clinicians' skills, encompassing test and service availability.
Parastomal hernia: an unsolved problem of herniology
Authors: Vlasov A. V. , Panyushkin A. V. 
Published: October 2024

INTRODUCTION. The frequency of parastomal hernias reaches 58 % and occurs with any type of stoma.The OBJECTIVE was to analyze the results of open retromuscular prosthetic repair of the abdominal wall with posterior separation of components in the treatment of parastomal hernias.METHODS AND MATERIALS. Between 2019 and 2023, 11 patients with end colostomies and parastomal hernias were operated on. The median age of patients was 72 years. There were 10 women, 1 man. According to the classification of the European Society of Herniology (2014), the distribution was as follows: type I – there were no patients, type II – 1 patient, type III – 5 patients, type IV – 5 patients. One patient had a recurrent parastomal hernia. All patients underwent open retromuscular prosthetic repair of the abdominal wall with posterior separation of components and formation of a colostomy in the same place.RESULTS. The treatment results were studied in 10 patients. There was fatal outcome in 1 patient with a type IV parastomal hernia due to infection with the development of necrotizing fasciitis and cellulitis of the abdominal wall. In one case, necrosis of the colostomy occurred, which required laparoscopic mobilization and re-formation of the colostomy. Long-term results were monitored in 9 patients over a period of 1 to 4 years. Recurrence occurred in 4 patients: 1 patient with type III parastomal hernia and 5 patients with type IV (two patients had 2 relapses). With repeated relapses, in one case, there was a pinching of the section of the small intestine in the paracolostomy openingCONCLUSION. The results of treatment of parastomal hernias in our clinic were largely disappointing. Some success can be noted only in the treatment of type III parastomal hernias.
Short-term results of surgical treatment of brachial artery injuries in patients with upper limb injury
Authors: Makar L. V. , Borodulin A. V. , Kolesnichenko A. Yu. , Kazarenko A. G. , Mokrushin K. S. , Abakarov G. Zh. , Shchukina O. M. , Chernyshev D. A. , Vladimirov P. А. , Vakhitov K. M. , Bedrov A. Ya. 
Published: October 2024

The OBJECTIVE was to study the short-term results of surgical treatment of patients with brachial artery injury in peacetime upper limb injury.METHODS AND MATERIALS. This study presents the short-term results of surgical treatment of 61 patients with brachial artery injury in peacetime upper limb injury. The study included 33 patients who were admitted to the City Hospital of St. Martyr Elizabeth in St. Petersburg from 2011 to 2022 and 28 patients who were admitted to Hospitals in the Leningrad Region from 2017 to 2022.RESULTS. All 61 patients underwent emergency surgery: autovenous prosthetics of the brachial artery was performed in 46 patients, an end-to-end anastomosis was formed in 10 patients, and a lateral suture was applied to 5 patients. In the early postoperative period, there were 3 thrombosis of the reconstruction zone, 1 amputation of a limb, 1 fatal outcome from severe blood loss.CONCLUSION. Upper limb injury with brachial artery injury without specialized assistance can lead to disability and even death of a patient, therefore requires emergency intervention by a vascular surgeon to stop bleeding, restore the main blood flow and stop limb ischemia.
Experience in using «anchor marks» for preoperative marking of small-diameter intra-pulmonary peripheral neoplasms
Authors: Dmitrochenko I. V. , Fufaev E. E. , Dzidzava I. I. , Yasyuchenya D. A. , Barinov O. V. , Popov V. A. , Kotiv B. A. , Safronova A. A. 
Published: October 2024

The OBJECTIVE was to evaluate the effectiveness of the use of preoperative transthoracic insertion of an «anchor mark» as a marker of a small intra-pulmonary pathological site for performing atypical videothoracoscopic resection (biopsy).MATERIALS AND METHODS. The study included 15 patients with solitary peripheral lung neoplasms of small diameter (8 [6; 10] mm). All neoplasms were located in the intermediate zone of the pulmonary parenchyma.RESULTS. In 9 (60 %) patients, according to cito-biopsy data, tumor cells were detected in the studied preparation, which served as a reason for performing endovideosurgical anatomical lung resection – lobectomy, in 2 (13.3 %) patients, hamartoma was detected and, thus, atypical lung resection proved to be a sufficient volume of surgical intervention, in 4 (26.7 %) patients, areas of local pneumofibrosis were verified, which made it possible to complete surgery at the diagnostic stage. The average duration of marking of the pathological focus was 25 minutes, atypical videothoracoscopic lung resection was 30 minutes. There were no access conversions.CONCLUSION. Preoperative transthoracic marking by means of the «anchor marks» system is a safe and highly effective navigation method for atypical resection (videothoracoscopic biopsy) of small-diameter lung neoplasms.
Immediate results of extrapleural thoracoplasty in patients with destructive pulmonary tuberculosis and HIV infection
Authors: Yakovlev G. A. , Ionov P. M. , Alkaz D. V. , Elkin A. V. , Boyarkin G. M. , Basek T. S. 
Published: October 2024

The OBJECTIVE was to study the features of intraoperative and postoperative periods as well as the immediate results of extrapleural thoracoplasty among patients with destructive tuberculosis in combination with human immunodeficiency virus (HIV).METHODS AND MATERIALS. A retrospective analysis of the results of extrapleural thoracoplasty for destructive pulmonary tuberculosis was performed in 46 patients with HIV infection and in 44 patients with tuberculosis without HIV infection. The groups were comparable in age and gender composition. The following variables were analyzed: the duration of the operation, the volume of blood loss, the volume of loss through drainage, the duration of postoperative drainage, the severity of postoperative pain syndrome, intra- and postoperative complications.RESULTS. We noted that, despite the longer tuberculosis duration, the frequency of bacterial excretion, the prevalence of extensive drug resistance (XDR), immune dysfunctions, high prevalence of drug addiction and chronic viral hepatitis, the results of extrapleural thoracoplasty in patients with HIV infection did not significantly differ from the results of patients without HIV infection operated for destructive pulmonary tuberculosis. Postoperative complications were few, temporary and treatable, and there was no postoperative mortality.CONCLUSION. Extrapleural thoracoplasty in patients with destructive pulmonary tuberculosis and HIV infection is not accompanied by severe, life-threatening complications. It also contributes to a significant reduction in destruction cavities in half of the operated patients. This operation does not make the course of HIV infection more difficult.
Treatment tactics for acute anterior cruciate ligament ruptures
Authors: Pupynin D. Yu. , Lychagin A. V. , Gritsyuk A. A. 
Published: October 2024

The OBJECTIVE was to study the 5-year results of dynamic intraligamentous stabilization compared with early knee anterior cruciate ligament (ACL) repair.METHODS AND MATERIALS. We carried out the study and statistical analysis of the treatment of 72 patients (47 men and 25 women), average age 30.9±8.5 years (min. 18 max, 45 years), with injury duration from 3 to 21 days (aver-age – 10.6±5.0 days) with ACL injury, activity level on the Tegner scale before injury not lower than 5 (1–9), average value 5.8±0.9 points. In group I (39 patients), with arthroscopic diagnosis and detection of separation from the femur with preservation of the synovial membrane, DIS was performed; in group II (control. 33 patients), early ACL repair was performed.RESULTS. Pain syndrome according to VAS after 12 months was 1.1±0.8 and 1.3±1.0 points (p=0.340). Patient satisfaction with the operation after 12 months in group I was 8.0±0.8 points, in group II – 7.4±0.8 (p=0.003). Tegner test at 12 months after surgery in group I was 6.5±0.9 points, in group II was 6.3±0.8 (p=0.014). Results on the Lysholm scale at 12 months: 91.1±2.2 and 88.6±3.5 points (p=0.001). During the dynamic study for 5 years, relapses of anteromedial instability of the knee joint were detected in 10 patients, which amounted to 13.9%, while in 4 patients in group I (10.3%), in group II in 6 patients (18.2%).CONCLUSION. Dynamic intraligamentous stabilization, in comparison with early anterior cruciate ligament plastic, shows a more rapid recovery of the level of physical activity in the next year after surgery; and in the long-term period, in terms of the number of relapses of instability, the results are no worse, which may influence changes in the algorithm for choosing surgical treatment.
Application of a special nasointestinal tube in the treatment of acute pancreatitis
Authors: Kashintsev A. A. , Kokhanenko N. Yu. , Proutski V. Yu. , Anisimov S. V. , Nadeeva A. A. , Ulyanov Yu. N. , Ivanov A. L. 
Published: October 2024

Conservative treatment of severe and moderately severe acute pancreatitis (AP) with a focus on reducing suppurative complications poses a challenging task. The early initiation of enteral nutrition plays a crucial role in improving AP treatment outcomes. This case presentation illustrates an original method of duodenal drainage and intestinal tube feeding.A case of a patient with moderately severe acute pancreatitis and a relatively high risk of a fatal outcome is presented. Positive therapeutic effects were achieved through the innovative method of selective feeding with duodenal isolation. Percutaneous drainage of the abdominal cavity under ultrasound control for enzymatic peritonitis, coupled with early artificial feeding, successfully prevented infection and the development of multiorgan failure.The developed method of duodenal content aspiration and early jejunal tube feeding has demonstrated both effectiveness and safety.
AI-Driven Watermarking Technique for Safeguarding Text Integrity in the Digital Age
Authors: Rasane Atharva 
Published: October 2024

The internet’s growth has led to a surge in text usage. Now, with public access to generative AI models like ChatGPT/Bard, identifying the source is vital. This is crucial due to concerns about copyright infringement and plagiarism. Moreover, it is essential to differentiate AI-generated text to curb misinformation from AI model hallucinations.In this paper, we explore text watermarking as a potential solution, focusing on plain ASCII text in English. We investigate techniques including physical watermarking (e.g., UniSpaCh by Por et al.), which modifies text to hide a binary message using Unicode Spaces, and logical watermarking (e.g., word context by Jalil et al.), which generates a watermark key via a defined process. While logical watermarking is difficult to break but undetectable without prior knowledge, physical watermarks are easily detected but also easy to break.This paper presents a unique physical watermarking technique based on word substitution to address these challenges. The core idea is that AI models consistently produce the same output for the same input. Initially, we replaced every i-th word (for example, every 5th word) with a “[MASK],” a placeholder token used in natural language processing models to indicate where a word has been removed and needs to be predicted. Then, we used a BERT model to predict the most probable token in place of “[MASK].” The resulting text constitutes the watermarked text. To verify, we reran the algorithm on the watermarked text and compared the input and output for similarity.The Python implementation of the algorithm in this paper employs models from the HuggingFace Transformer Library, namely “bert-base-uncased” and “distilroberta-base”. The “[MASK]” placeholder was generated by splitting the input string using the split() function and then replacing every 5th element in the list with “[MASK]”. This modified list served as the input text for the BERT model, where the output corresponding to each “[MASK]” was replaced accordingly. Finally, applying the join() function to the list produces the watermarked text.This technique tends to generate nearly invisible watermarked text, preserving its integrity or completely changing the meaning of the text based on how similar the text is to the training dataset of BERT. This was observed when the algorithm was run on the story of Red Riding Hood, where its meaning was altered. However, the nature of this watermark makes it extremely difficult to break due to the black-box nature of the AI model.
Making Research Data Flow With Python
Authors: Borrow Josh , Plante Paul La , Aguirre James , Williams Peter K. G. 
Published: October 2024

The increasing volume of research data in fields such as astronomy, biology,
and engineering necessitates efficient distributed data management.
Traditional commercial solutions are often unsuitable for the decentralized
infrastructure typical of academic projects. This paper presents the
Librarian, a custom framework designed for data transfer in large academic
collaborations, designed for the Simons Observatory (SO) as a ground up
re-architechture of a previous astronomical data management tool called the
‘HERA Librarian’ from which it takes its name. SO is a new-generation
observatory designed for observing the Cosmic Microwave Background, and is
located in the Atacama desert in Chile at over 5000 meters of elevation.Existing tools like Globus Flows, iRODS, Rucio, and Datalad were evaluated
but were found to be lacking in automation or simplicity. Librarian
addresses these gaps by integrating with Globus for efficient data transfer
and providing a RESTful API for easy interaction. It also supports transfers
through the movement of physical media for environments with intermittent
connectivity.Using technologies like Python, FastAPI, and SQLAlchemy, the Librarian
ensures robust, scalable, and user-friendly data management tailored to the
needs of large-scale scientific projects. This solution demonstrates an
effective method for managing the substantial data flows in modern ‘big
science’ endeavors.
Ecological and Spatial Influences on the Genetics of Cumacea (Crustacea: Peracarida) in the Northern North Atlantic
Authors: Gagnon Justin , Tahiri Nadia 
Published: October 2024

The peracarid taxon Cumacea is an essential indicator of benthic quality in marine ecosystems. This study investigated the influence of environmental (i.e., biological or ecosystemic), climatic (i.e., meteorological or atmospheric), and spatial (i.e., geographic or regional) variables on their genetic variability and adaptability in the Northern North Atlantic, focusing on Icelandic waters. We analyzed partial sequences of the 16S rRNA mitochondrial gene from 62 Cumacea specimens. Using the aPhyloGeo software, we compared these sequences with relevant variables such as latitude (decimal degree) at the end of sampling, wind speed (m/s) at the start of sampling, O2 concentration (mg/L), and depth (m) at the start of sampling.Our analyses revealed variability in spatial and biological variables, reflecting the diversity of ecological requirements and benthic habitats. The most common Cumacea families, Diastylidae and Leuconidae, suggest adaptations to various marine environments. Phylogeographic analysis showed a divergence between specific genetic sequences and two habitat variables: wind speed (m/s) at the start of sampling and O2 concentration (mg/L). This observation may indicate the possibility of varying local adaptations in response to these fluctuating conditions.These results reinforce the importance of further research into the relationship between Cumacea genetics and global environmental variables to interpret the evolutionary dynamics and adaptation of these deep-sea organisms. This study sheds much-needed light on the acclimatization of invertebrates to climate change, anthropogenic pressures, and marine habitat management, potentially contributing to the evolution of more effective conservation strategies and policies to protect these vulnerable ecosystems.The aPhyloGeo Python package is freely and publicly available on GitHub and PyPi, providing an invaluable tool for future research.
Cyanobacteria detection in small, inland water bodies with CyFi
Authors: Dorne Emily , Wetstone Katie , Cerquera Trista Brophy , Gupta Shobhana 
Published: October 2024

Harmful algal blooms (HABs) pose major health risks to human and aquatic life. Remote sensing-based methods exist to automatically detect large, slow-moving HABs in the ocean, but fall short for smaller, more dynamic blooms in critical inland water bodies like lakes, reservoirs, and rivers.CyFi is an open-source Python package that enables detection of cyanobacteria in inland water bodies using 10-30m Sentinel-2 imagery and a computationally efficient tree-based machine learning model. CyFi enables water quality and public health managers to conduct high level assessments of water bodies of interest and identify regions in which to target monitoring and responsive actions to protect public health.CyFi was developed in three phases. A machine learning competition leveraged the diverse skills and creativity of data science experts to surface promising approaches for cyanobacteria detection from remote sensed data. Subsequent user interviews and model iteration resulted in a deployment-ready open-source package designed to meet user workflow needs and decision-making priorities. This process illustrates a replicable pathway for developing powerful machine learning tools in domain-specific areas.
ITK-Wasm
Authors: McCormick Matthew , Elliott Paul 
Published: October 2024

In recent years, WebAssembly (Wasm) has emerged as a widely-supported technology that offers high performance, compact binary size, support for multiple languages, hardware independence, security, and universal platform support, enabling developers to bring near-native speeds and portability to applications for the web and beyond. ITK-Wasm brings WebAssembly’s capabilities to scientific computing by combining the Insight Toolkit (ITK) and WebAssembly to enable high-performance spatial analysis across programming languages and hardware architectures.In the scientific Python ecosystem, ITK-Wasm packages work in a web browser via Pyodide but also in system-level environments through the WebAssembly System Interface (WASI). ITK-Wasm bridges WebAssembly with scientific Python through simple, fundamental Python and NumPy-based data structures and Pythonic function interfaces. These interfaces can be accelerated through graphics processing units (GPU) or neural processing unit (NPU) implementations when available.Beyond Python, ITK-Wasm’s integration of the WebAssembly Component Model launches scientific computing into a new world of interoperability, enabling the creation of accessible and sustainable multi-language projects that are easily distributed anywhere.