bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spontaneous retroperitoneal haematoma in severe dengue: A case report
Authors: Ab Rahman Siti Soraya , Nik Mazian Assyifaa , Samad Sarah Zulaikha 
Published: October 2023

AbstractDengue is endemic in over 100 countries worldwide, predominantly in the subtropical and tropical regions and the incidence has been increasing globally. Patients with severe dengue may develop massive bleeding, disseminated intravascular coagulopathy and multi‐organ failure. Bleeding may occur in various body cavities and muscles; however, bleeding in the retroperitoneal space is uncommon. We report a case of a 37‐year‐old gentleman who presented with a 4‐day history of fever associated with chills and rigours. On Day 6 of illness, he complained of left lumbar and left iliac fossa pain which was aggravated by movement. A computed tomography angiography scan of the abdomen showed the presence of a retroperitoneal haematoma, left iliopsoas and quadratus lumbarum intramuscular haematoma with active bleeding and left abdominal wall muscles haematoma. His condition gradually improved after multiple blood transfusions and he gained full recovery. Spontaneous retroperitoneal haematoma is an uncommon complication of severe dengue infection. Early diagnosis based on high index of clinical suspicion using appropriate imaging will aid in prompt management of these cases and may prevent deaths.
Application of imaging spectroscopy, SEM-EDS and DNA analysis for monitoring the preservation status of a manuscript of the first decade of 19th century
Authors: Kokla Vasiliki , Batrinou Anthimia , Papatheodorou Spyros , Houhoula Dimitra , Panagiaris George , Tselikas Agamemnon , Karabotsos Athanassios 
Published: October 2023

AbstractThis paper presents an interdisciplinary approach on the preservation status of a manuscript made in the early nineteenth century on paper support. This approach was based on the analysis of the pigments and inks, as well as the damage of the manuscript, which was provoked by biological attack. This analysis was accomplished with the application of innovating techniques such as imaging spectroscopy using high resolution cameras and DNA analysis. The use of new technologies from diverse science can provide useful information on the inks and pigments as well as the type of biological agents found in the manuscript. Furthermore, apart from the knowledge about the inks and pigments, important elements can be retrieved on their preservation status. The aim of this research is the combined use of the detected information on the types of inks and pigments with the biological investigation in order to trace damage caused by biological attack and to investigate the causative agent of this attack. For this reason, imaging techniques, SEM/EDS analysis were applied to the inks and pigments as well as a microbiologic and molecular analysis of the fungi found on the pigments of manuscript.
Iceberg Hashing: Optimizing Many Hash-Table Criteria at Once
Authors: Bender Michael A. , Conway Alex , Farach-Colton Martín , Kuszmaul William , Tagliavini Guido 
Published: October 2023

Despite being one of the oldest data structures in computer science, hash tables continue to be the focus of a great deal of both theoretical and empirical research. A central reason for this is that many of the fundamental properties that one desires from a hash table are difficult to achieve simultaneously; thus many variants offering different trade-offs have been proposed.

This article introduces Iceberg hashing, a hash table that simultaneously offers the strongest known guarantees on a large number of core properties. Iceberg hashing supports constant-time operations while improving on the state of the art for space efficiency, cache efficiency, and low failure probability. Iceberg hashing is also the first hash table to support a load factor of up to
1 - o(1)
while being stable, meaning that the position where an element is stored only ever changes when resizes occur. In fact, in the setting where keys are Θ (log
n
) bits, the space guarantees that Iceberg hashing offers, namely that it uses at most

\(\log \binom{|U|}{n} + O(n \log \ \text{log} n)\)

bits to store
n
items from a universe
U
, matches a lower bound by Demaine et al. that applies to any stable hash table.

Iceberg hashing introduces new general-purpose techniques for some of the most basic aspects of hash-table design. Notably, our indirection-free technique for dynamic resizing, which we call waterfall addressing, and our techniques for achieving stability and very-high probability guarantees, can be applied to any hash table that makes use of the front-yard/backyard paradigm for hash table design.
Circulating Tumor DNA Analysis in Advanced Urothelial Carcinoma: Insights from Biological Analysis and Extended Clinical Follow-up
Authors: Lindskrog Sia V. , Birkenkamp-Demtröder Karin , Nordentoft Iver , Laliotis George , Lamy Philippe , Christensen Emil , Renner Derrick , Andreasen Tine G. , Lange Naja , Sharma Shruti , ElNaggar Adam C. , Liu Minetta C. , Sethi Himanshu , Aleshin Alexey , Agerbæk Mads , Jensen Jørgen B. , Dyrskjøt Lars 
Published: October 2023

Abstract

Purpose:
To investigate whether circulating tumor DNA (ctDNA) assessment in patients with muscle-invasive bladder cancer predicts treatment response and provides early detection of metastatic disease.

Experimental Design:
We present full follow-up results (median follow-up: 68 months) from a previously described cohort of 68 neoadjuvant chemotherapy (NAC)-treated patients who underwent longitudinal ctDNA testing (712 plasma samples). In addition, we performed ctDNA evaluation of 153 plasma samples collected before and after radical cystectomy (RC) in a separate cohort of 102 NAC-naïve patients (median follow-up: 72 months). Total RNA sequencing of tumors was performed to investigate biological characteristics of ctDNA shedding tumors.

Results:
Assessment of ctDNA after RC identified metastatic relapse with a sensitivity of 94% and specificity of 98% using the expanded follow-up data for the NAC-treated patients. ctDNA dynamics during NAC was independently associated with patient outcomes when adjusted for pathologic downstaging (HR = 4.7; P = 0.029). For the NAC-naïve patients, ctDNA was a prognostic predictor before (HR = 3.4; P = 0.0005) and after RC (HR = 17.8; P = 0.0002). No statistically significant difference in recurrence-free survival for patients without detectable ctDNA at diagnosis was observed between the cohorts. Baseline ctDNA positivity was associated with the Basal/Squamous (Ba/Sq) subtype and enrichment of epithelial-to-mesenchymal transition and cell cycle–associated gene sets.

Conclusions:
ctDNA is prognostic in NAC-treated and NAC-naïve patients with more than 5 years follow-up and outperforms pathologic downstaging in predicting treatment efficacy. Patients without detectable ctDNA at diagnosis may benefit significantly less from NAC, but additional studies are needed.
Predicting Mammogram Screening Follow Through with Electronic Health Record and Geographically Linked Data
Authors: Davis Matthew , Simpson Kit , Lenert Leslie A. , Diaz Vanessa , Alekseyenko Alexander V. 
Published: October 2023

Abstract

Cancer is the second leading cause of death in the United States, and breast cancer is the fourth leading cause of cancer-related death, with 42,275 women dying of breast cancer in the United States in 2020. Screening is a key strategy for reducing mortality from breast cancer and is recommended by various national guidelines. This study applies machine learning classification methods to the task of predicting which patients will fail to complete a mammogram screening after having one ordered, as well as understanding the underlying features that influence predictions. The results show that a small group of patients can be identified that are very unlikely to complete mammogram screening, enabling care managers to focus resources.

Significance:
The motivation behind this study is to create an automated system that can identify a small group of individuals that are at elevated risk for not following through completing a mammogram screening. This will enable interventions to boost screening to be focused on patients least likely to complete screening.
Tracer Study of the Nursing Graduates in a State College
Authors: Austria Jayson S. 
Published: October 2023

Introduction: This graduate tracer study aimed to improve the nursing program in a state college. Method: It used descriptive survey collect the nursing graduates' demographic, educational, and employment profiles, as well as their feedbacks. The study used 60% representative stratified and snowball samplings. Findings presented in frequency distribution tables. Feedbacks were grouped into themes. Results: The demographic profile showed varied age from 20 to 40 years old, who were largely female. The educational profile showed fluctuating nurse licensure examination percentage, and a large number who were not actively involved in continuing professional development. The employment profile showed a large number of graduates who were not employed in nursing related jobs and without permanent employment status. Conclusion: Thus, these findings corroborated the graduates' feedbacks that to produce quality graduates for the labor market, program offering improvement in terms of faculty, curriculum and instruction, library, and physical facilities is needed.
Calibrated Interpretation: Confidence Estimation in Semantic Parsing
Authors: Stengel-Eskin Elias , Van Durme Benjamin 
Published: October 2023

AbstractSequence generation models are increasingly being used to translate natural language into programs, i.e., to perform executable semantic parsing. The fact that semantic parsing aims to predict programs that can lead to executed actions in the real world motivates developing safe systems. This in turn makes measuring calibration—a central component to safety—particularly important. We investigate the calibration of popular generation models across four popular semantic parsing datasets, finding that it varies across models and datasets. We then analyze factors associated with calibration error and release new confidence-based challenge splits of two parsing datasets. To facilitate the inclusion of calibration in semantic parsing evaluations, we release a library for computing calibration metrics.1
Recent Increase in a Recurrent Pan-Atlantic Wave Pattern Driving Concurrent Wintertime Extremes
Authors: Kornhuber Kai , Messori Gabriele 
Published: October 2023

Abstract
Wintertime extremes such as cold spells and heavy precipitation can have severe socioeconomic impacts, disrupting critical infrastructures and affecting human well-being. Here, we relate the occurrence of local and concurrent cold or wet wintertime extremes in North America and Europe to a recurrent, quasi-hemispheric wave-4 Rossby wave pattern. We identify this pattern as a fundamental mode of the Northern Hemisphere (NH) winter circulation, since wave 4 exhibits phase-locking behavior. Thus, the associated atmospheric circulation and surface anomalies reoccur over the same locations when the pattern’s wave amplitude is high. The wave pattern is most pronounced over the pan-Atlantic region, and increases the probability of extreme cold or wet events by up to 300% in certain areas of North America and Europe, as well as favoring their concurrence at different locations. High-amplitude wave-4 events have increased significantly in frequency over the past four decades (1979–2021), although no clear evidence is found relating this to modes or patterns of climate variability. The identified wave pattern may provide pathways for early prediction of local and concurrent cold or wet wintertime extremes in North America and Europe.
Resistance to PRMT5-targeted therapy in mantle cell lymphoma
Authors: Long Mackenzie Elizabeth , Koirala Shirsha , Sloan Shelby , Brown-Burke Fiona , Weigel Christoph , Villagomez Lynda , Corps Kara , Sharma Archisha , Hout Ian , Harper Margaret , Helmig-Mason JoBeth , Tallada Sheetal , Chen Zhengming , Scherle Peggy , Vaddi Kris , Chen-Kiang Selina , Di Liberto Maurizio , Meydan Cem , Foox Jonathan , Butler Daniel , Mason Christopher , Alinari Lapo , Blaser Bradley W. , Baiocchi Robert 
Published: October 2023

Abstract
Mantle cell lymphoma (MCL) is an incurable B-cell non-Hodgkin lymphoma, and patients who relapse on targeted therapies have poor prognosis. Protein arginine methyltransferase 5 (PRMT5), an enzyme essential for B-cell transformation, drives multiple oncogenic pathways and is overexpressed in MCL. Despite the antitumor activity of PRMT5 inhibition (PRT-382/PRT-808), drug resistance was observed in a patient-derived xenograft (PDX) MCL model. Decreased survival of mice engrafted with these PRMT5 inhibitor–resistant cells vs treatment-naive cells was observed (P = .005). MCL cell lines showed variable sensitivity to PRMT5 inhibition. Using PRT-382, cell lines were classified as sensitive (n = 4; 50% inhibitory concentration [IC50], 20-140 nM) or primary resistant (n = 4; 340-1650 nM). Prolonged culture of sensitive MCL lines with drug escalation produced PRMT5 inhibitor–resistant cell lines (n = 4; 200-500 nM). This resistant phenotype persisted after prolonged culture in the absence of drug and was observed with PRT-808. In the resistant PDX and cell line models, symmetric dimethylarginine reduction was achieved at the original PRMT5 inhibitor IC50, suggesting activation of alternative resistance pathways. Bulk RNA sequencing of resistant cell lines and PDX relative to sensitive or short-term–treated cells, respectively, highlighted shared upregulation of multiple pathways including mechanistic target of rapamycin kinase [mTOR] signaling (P &lt; 10-5 and z score &gt; 0.3 or &lt; 0.3). Single-cell RNA sequencing analysis demonstrated a strong shift in global gene expression, with upregulation of mTOR signaling in resistant PDX MCL samples. Targeted blockade of mTORC1 with temsirolimus overcame the PRMT5 inhibitor–resistant phenotype, displayed therapeutic synergy in resistant MCL cell lines, and improved survival of a resistant PDX.
Mechanism of Shugan Yidan fang, a Chinese herbal formula, in rat model of premature ejaculation
Authors: Han Qiang , Guo Jun , Wang Renyuan , Li Jiangminzi , Wang Fu , Gao Qinghe , Zhang Jiwei , Wang Hetian , Zeng Yin 
Published: October 2023

Abstract
Background
Premature ejaculation (PE) is one of the most common forms of sexual dysfunction in men, and multimodal therapeutic regimens should be considered to treat the condition. We developed a Chinese medicine herbal medicine, Shugan Yidan fang that had a significant clinical effect on PE patients, extending the time between penetration and ejaculation. However, the mechanism of this formula remains unclear. There is evidence that PE is associated with peripheral neuropathology, and the actions of dopamine (DA) and 5-hydroxytryptamine (5-HT). The aim of this study was to investigate the mechanism of Shugan Yidan fang’s effect on PE through the relationship between sexual behavioristics and the level of neurotransmitters and dopamine receptors (DARs).

Results
We showed that the male PE groups had a significant PE phenotype compared to healthy rats. Treatment with Shugan Yidan fang improved the behavioristics of the PE rats, and reduced the expression of DAR mRNA and protein while improving dopamine transporter levels.

Conclusions
Our study provided evidence for the beneficial effect of Shugan Yidan fang in PE therapy, and proposed a preliminary potential mechanism for the clinical application of the formula.
HoCoRT: host contamination removal tool
Authors: Rumbavicius Ignas , Rounge Trine B. , Rognes Torbjørn 
Published: October 2023

Abstract
Background
Shotgun metagenome sequencing data obtained from a host environment will usually be contaminated with sequences from the host organism. Host sequences should be removed before further analysis to avoid biases, reduce downstream computational load, or ensure privacy in the case of a human host. The tools that we identified, as designed specifically to perform host contamination sequence removal, were either outdated, not maintained, or complicated to use. Consequently, we have developed HoCoRT, a fast and user-friendly tool that implements several methods for optimised host sequence removal. We have evaluated the speed and accuracy of these methods.

Results
HoCoRT is an open-source command-line tool for host contamination removal. It is designed to be easy to install and use, offering a one-step option for genome indexing. HoCoRT employs a variety of well-known mapping, classification, and alignment methods to classify reads. The user can select the underlying classification method and its parameters, allowing adaptation to different scenarios. Based on our investigation of various methods and parameters using synthetic human gut and oral microbiomes, and on assessment of publicly available data, we provide recommendations for typical datasets with short and long reads.

Conclusions
To decontaminate a human gut microbiome with short reads using HoCoRT, we found the optimal combination of speed and accuracy with BioBloom, Bowtie2 in end-to-end mode, and HISAT2. Kraken2 consistently demonstrated the highest speed, albeit with a trade-off in accuracy. The same applies to an oral microbiome, but here Bowtie2 was notably slower than the other tools. For long reads, the detection of human host reads is more difficult. In this case, a combination of Kraken2 and Minimap2 achieved the highest accuracy and detected 59% of human reads. In comparison to the dedicated DeconSeq tool, HoCoRT using Bowtie2 in end-to-end mode proved considerably faster and slightly more accurate. HoCoRT is available as a Bioconda package, and the source code can be accessed at https://github.com/ignasrum/hocort along with the documentation. It is released under the MIT licence and is compatible with Linux and macOS (except for the BioBloom module).
Transcriptomic landscape of posterior regeneration in the annelid Platynereis dumerilii
Authors: Paré Louis , Bideau Loïc , Baduel Loeiza , Dalle Caroline , Benchouaia Médine , Schneider Stephan Q. , Laplane Lucie , Clément Yves , Vervoort Michel , Gazave Eve 
Published: October 2023

Abstract
Background
Restorative regeneration, the capacity to reform a lost body part following amputation or injury, is an important and still poorly understood process in animals. Annelids, or segmented worms, show amazing regenerative capabilities, and as such are a crucial group to investigate. Elucidating the molecular mechanisms that underpin regeneration in this major group remains a key goal. Among annelids, the nereididae Platynereis dumerilii (re)emerged recently as a front-line regeneration model. Following amputation of its posterior part, Platynereis worms can regenerate both differentiated tissues of their terminal part as well as a growth zone that contains putative stem cells. While this regeneration process follows specific and reproducible stages that have been well characterized, the transcriptomic landscape of these stages remains to be uncovered.

Results
We generated a high-quality de novo Reference transcriptome for the annelid Platynereis dumerilii. We produced and analyzed three RNA-sequencing datasets, encompassing five stages of posterior regeneration, along with blastema stages and non-amputated tissues as controls. We included two of these regeneration RNA-seq datasets, as well as embryonic and tissue-specific datasets from the literature to produce a Reference transcriptome. We used this Reference transcriptome to perform in depth analyzes of RNA-seq data during the course of regeneration to reveal the important dynamics of the gene expression, process with thousands of genes differentially expressed between stages, as well as unique and specific gene expression at each regeneration stage. The study of these genes highlighted the importance of the nervous system at both early and late stages of regeneration, as well as the enrichment of RNA-binding proteins (RBPs) during almost the entire regeneration process.

Conclusions
In this study, we provided a high-quality de novo Reference transcriptome for the annelid Platynereis that is useful for investigating various developmental processes, including regeneration. Our extensive stage-specific transcriptional analysis during the course of posterior regeneration sheds light upon major molecular mechanisms and pathways, and will foster many specific studies in the future.
Next-generation fungal identification using target enrichment and Nanopore sequencing
Authors: Yu Pei-Ling , Fulton James C. , Hudson Owen H. , Huguet-Tapia Jose C. , Brawner Jeremy T. 
Published: October 2023

Abstract
Background
Rapid and accurate pathogen identification is required for disease management. Compared to sequencing entire genomes, targeted sequencing may be used to direct sequencing resources to genes of interest for microbe identification and mitigate the low resolution that single-locus molecular identification provides. This work describes a broad-spectrum fungal identification tool developed to focus high-throughput Nanopore sequencing on genes commonly employed for disease diagnostics and phylogenetic inference.

Results
Orthologs of targeted genes were extracted from 386 reference genomes of fungal species spanning six phyla to identify homologous regions that were used to design the baits used for enrichment. To reduce the cost of producing probes without diminishing the phylogenetic power, DNA sequences were first clustered, and then consensus sequences within each cluster were identified to produce 26,000 probes that targeted 114 genes. To test the efficacy of our probes, we applied the technique to three species representing Ascomycota and Basidiomycota fungi. The efficiency of enrichment, quantified as mean target coverage over the mean genome-wide coverage, ranged from 200 to 300. Furthermore, enrichment of long reads increased the depth of coverage across the targeted genes and into non-coding flanking sequence. The assemblies generated from enriched samples provided well-resolved phylogenetic trees for taxonomic assignment and molecular identification.

Conclusions
Our work provides data to support the utility of targeted Nanopore sequencing for fungal identification and provides a platform that may be extended for use with other phytopathogens.