bluuebunny/crossref_metadata_2025_split huggingface dataset:
Efficient similar waveform search using short binary codes obtained through a deep hashing technique
Authors: Naoi Makoto , Hirano Shiro 
Published: February 2024

SUMMARY
A similar waveform search plays a crucial role in seismology for detecting seismic events, such as small earthquakes and low-frequency events. However, the high computational costs associated with waveform cross-correlation calculations represent bottlenecks during the analysis of long, continuous records obtained from numerous stations. In this study, we developed a deep-learning network to obtain 64-bit hash codes containing information on seismic waveforms. Using this network, we performed a similar waveform search for ∼35 million moving windows developed for the 30 min waveforms recorded continuously at 10 MHz sampling rates using 16 acoustic emission transducers during a laboratory hydraulic fracturing experiment. The sampling points of each channel corresponded to those of the 5.8-yr records obtained from typical seismic observations at 100 Hz sampling rates. Of the 35 million windows, we searched for windows with small average Hamming distances among the hash codes of 16 channel waveforms against template hash codes of 6057 events that were catalogued using conventional autoprocessing techniques. The calculation of average Hamming distances is 1430–1530 times faster than that of the corresponding network correlation. This hashing-based template matching enabled the detection of 23 462 additional events. We also demonstrated the feasibility of the hashing-based autocorrelation analysis, where similar event pairs were extracted without templates, by calculating the average Hamming distances for all possible pairs of the ∼35 million windows. This calculation required only 15.5 h under 120 thread parallelization. This deep hashing approach significantly reduced the required memory compared with locality-sensitive hashing approaches based on random permutations, enabling similar waveform searching on a large-scale data set.
Distancing through peacekeeping: global peacekeeping assemblages and the Gambian armed forces
Authors: Dwyer Maggie 
Published: February 2024

Abstract
This article contributes to the understanding of incentives for peacekeeping contribution from non-democratic countries through the largely unexplored case of peacekeeping under authoritarian rule in The Gambia. It argues that President Yahya Jammeh (1994–2017) aimed to use peacekeeping to help keep himself in power, fitting a broader global pattern of peacekeeping for regime maintenance. However, the research also demonstrates that leadership's aims for peacekeeping can be misaligned with the experiences of soldiers. Rather than draw soldiers closer to the regime, the peacekeeping experience involved a distancing from the forces for Gambian soldiers when they returned home. The findings draw on interviews with returned peacekeepers and military decision makers in The Gambia, as well as publications from the armed forces and new public sources of information made available after the 2017 political transition. The article proposes that viewing the deployment experience as a global peacekeeping assemblage helps to understand the more subtle, yet significant, ways in which soldiers' views can shift following peacekeeping deployments.
Brief Communication: The Predictable Network Topology of Evolutionary Genomic Constraint
Authors: Wollenberg Valero Katharina C 
Published: February 2024

Abstract
Large-scale comparative genomics studies offer valuable resources for understanding both functional and evolutionary rate constraints. It is suggested that constraint aligns with the topology of genomic networks, increasing toward the center, with intermediate nodes combining relaxed constraint with higher contributions to the phenotype due to pleiotropy. However, this pattern has yet to be demonstrated in vertebrates. This study shows that constraint intensifies toward the network's center in placental mammals. Genes with rate changes associated with emergence of hibernation cluster mostly toward intermediate positions, with higher constraint in faster-evolving genes, which is indicative of a “sweet spot” for adaptation. If this trend holds universally, network node metrics could predict high-constraint regions even in clades lacking empirical constraint data.
Well-Being Therapy in systemic sclerosis outpatients: a randomized controlled trial
Authors: Romanazzo Sara , Ceccatelli Sara , Mansueto Giovanni , Sera Francesco , Guiducci Serena , Matucci Cerinic Marco , Cosci Fiammetta 
Published: February 2024

Abstract

Objectives
Systemic sclerosis (SSc) patients have psychological distress and poor well-being and need a tailored treatment. Psychological interventions, rarely tested for efficacy, showed poor benefits. The present randomized controlled trial tested the efficacy of Well-Being Therapy (WBT) in SSc patients.

Methods
Thirty-two outpatients were randomized (1:1) to WBT (n = 16) or Treatment As Usual (i.e. routine medical check-ups) (TAU) (n = 16). Primary outcome was well-being. Secondary outcomes included functional ability related to SSc, psychological distress, mental pain, suffering. All participants were assessed at baseline (T0). The WBT group was assessed after two months (end of WBT session 4) (T1), after four months (end of WBT session 8) (T2), after seven months (3-month follow-up) (T3) and after 10 months (6-month follow-up) (T4). The TAU group was assessed two (T1), four (T2), seven (T3) and ten (T4) months after baseline.

Results
WBT produced a significant improvement in subjective well-being (P ≤ 0.001), personal growth (P = 0.006), self-acceptance (P = 0.003) compared with TAU, maintained at T3 as what concerns subjective well-being (P = 0.012). WBT produced a greater decrease in psychological distress (P = 0.010), mental pain (P = 0.010), suffering (P ≤ 0.001) compared with TAU, maintained at T4 as what concerns suffering (P ≤ 0.001). Participants reported high satisfaction with WBT.

Conclusion
The study provides preliminary evidence on the benefits of WBT as short-term approach for in- and out-patient SSc healthcare paths. Studies with larger samples are needed to have the evidence for recommending WBT to SSc patients.
Increased type-I interferon level is associated with liver damage and fibrosis in primary sclerosing cholangitis
Authors: Salzmann Rebekka J.S. , Krötz Christina , Mocan Tudor , Mocan Lavinia P. , Grapa Cristiana , Rottmann Sophia , Reichelt Ramona , Keller Cindy M. , Langhans Bettina , Schünemann Frederik , Pohl Alexander , Böhler Thomas , Bersiner Käthe , Krawczyk Marcin , Milkiewicz Piotr , Sparchez Zeno , Lammert Frank , Gehlert Sebastian , Gonzalez-Carmona Maria A. , Willms Arnulf , Strassburg Christian P. , Kornek Miroslaw T. , Dold Leona , Lukacs-Kornek Veronika 
Published: February 2024

Background:
The level of type-I interferons (IFNs) in primary sclerosing cholangitis (PSC) was investigated to evaluate its association with disease activity and progression.

Methods:
Bioactive type-I IFNs were evaluated in a murine model of PSC and human patients’ sera using a cell-based reporter assay and ELISA techniques. In total, 57 healthy participants, 71 PSC, and 38 patients with primary biliary cholangitis were enrolled in this study.

Results:
Bioactive type-I IFNs were elevated in the liver and serum of multidrug resistance protein 2–deficient animals and showed a correlation with the presence of CD45+ immune cells and serum alanine transaminase levels. Concordantly, bioactive type-I IFNs were elevated in the sera of patients with PSC as compared to healthy controls (sensitivity of 84.51%, specificity of 63.16%, and AUROC value of 0.8267). Bioactive IFNs highly correlated with alkaline phosphatase (r=0.4179, p<0.001), alanine transaminase (r=0.4704, p<0.0001), and gamma-glutamyl transpeptidase activities (r=0.6629, p<0.0001) but not with serum bilirubin. In addition, patients with PSC with advanced fibrosis demonstrated significantly higher type-I IFN values. Among the type-I IFN subtypes IFNα, β and IFNω could be detected in patients with PSC with IFNω showing the highest concentration among the subtypes and being the most abundant among patients with PSC.

Conclusions:
The selectively elevated bioactive type-I IFNs specifically the dominating IFNω could suggest a novel inflammatory pathway that might also have a hitherto unrecognized role in the pathomechanism of PSC.
HBV DNA polymerase regulates tumor cell glycogen to enhance the malignancy of HCC cells
Authors: Zhao Xiaoqing , Wang Chunqing , Zhao Liqing , Tian Zhongzheng 
Published: February 2024

Background:
The essential function of HBV DNA polymerase (HBV-DNA-Pol) is to initiate viral replication by reverse transcription; however, the role of HBV-DNA-Pol in HBV-associated HCC has not been clarified. Glycogen phosphorylase L (PYGL) is a critical regulator of glycogenolysis and is involved in tumorigenesis, including HCC. However, it is unknown whether HBV-DNA-Pol regulates PYGL to contribute to HCC tumorigenesis.

Methods:
Bioinformatic analysis, real-time quantitative PCR, western blotting, and oncology functional assays were performed to determine the contribution of HBV-DNA-Pol and PYGL to HCC development and glycolysis. The mechanisms of co-immunoprecipitation and ubiquitination were employed to ascertain how HBV-DNA-Pol upregulated PYGL.

Results:
Overexpression of HBV-DNA-Pol enhanced HCC progression in vitro and in vivo. Mechanistically, HBV-DNA-Pol interacted with PYGL and increased PYGL protein levels by inhibiting PYGL ubiquitination, which was mediated by the E3 ligase TRIM21. HBV-DNA-Pol competitively impaired the binding of PYGL to TRIM21 due to its stronger binding affinity to TRIM21, suppressing the ubiquitination of PYGL. Moreover, HBV-DNA-Pol promoted glycogen decomposition by upregulating PYGL, which led to an increased flow of glucose into glycolysis, thereby promoting HCC development.

Conclusions:
Our study reveals a novel mechanism by which HBV-DNA-Pol promotes HCC by controlling glycogen metabolism in HCC, establishing a direct link between HBV-DNA-Pol and the Warburg effect, thereby providing novel targets for HCC treatment and drug development.
Improving Management: Novel Guidelines for Diagnosing Urinary Tract Infection in Infants
Authors: Khoury Lana , Schnapp Zeev , Konopnicki Muriel 
Published: February 2024

Background:
The diagnosis of urinary tract infection (UTI) in the pediatric field remains a topic of debate. In 2011, the American Academy of Pediatrics (AAP) introduced new guidelines for the diagnosis of UTI in patients 2–24 months old. However, concerns were raised regarding these guidelines.

Methods:
This is a retrospective data extraction study that included patients 0–6 months of age who were examined in the pediatric emergency department between 2016 and 2021 and had a urine culture. For each patient, we recorded the diagnosis documented in the medical records, the diagnosis based on the AAP and Israeli guidelines, and the diagnosis according to our 2 proposed protocols. We then compared the percentage of UTI diagnoses according to each diagnostic guideline.

Results:
A total of 1432 patients under the age of 6 months underwent urine culture testing during the study period. A total of 83 (5.81%) of these patients were diagnosed with UTI according to the AAP guidelines, 184 of the patients (12.8%) were diagnosed with UTI according to the Israeli guidelines, 102 (7.1%) and 109 (7.6%) of the patients were diagnosed with UTI according to our first and second proposed guidelines, respectively.

Conclusions:
We propose a new diagnostic method (guidelines II) that is suitable for patients older than 2 months, with obligatory criteria of abnormal urine test and a lower threshold for the colony count required for diagnosis compared to the AAP guidelines. Further research is required to examine the sensitivity and specificity of our proposed guidelines, so it may replace the current diverse guidelines.
Bleeding disorders in Saudi Arabia, causes and prevalence: a review
Authors: Belali Tareg M. 
Published: February 2024

As bleeding disorders are a worldwide health concern, Saudi Arabia is experiencing a notable prevalence of such disorders. Studying the frequency and cause of hemostatic disorders is the key to successful clinical interventions and instigating effective public policies that limit the spread of such disorders. The current review aims to highlight the major findings of the body of literature that has investigated the causes, prevalence, and major challenges associated with bleeding disorders in the country. The current review summarizes the major findings of different studies that have been conducted in Saudi Arabia regarding different bleeding disorders.
Multiple causes and symptoms of bleeding disorders have been reported by different studies. Some studies investigated the genetic aspect of bleeding disorders and revealed specific mutations in coagulation factor genes influencing the symptoms of different bleeding disorders. Moreover, rare bleeding disorders such as Glanzmann thrombasthenia and Henoch–Schönlein purpura, have been reported in different regions of Saudi Arabia. Combining clinical presentations, genetic factors, and epidemiological data, the current review of the literature provides a comprehensive insight into bleeding disorders in the kingdom. This will help in advancing the diagnostic capabilities and genetic counseling enhancing management strategies and therapeutic interventions benefiting bleeding disorder patients and the kingdom.
A role of platelet C-type lectin-like receptor-2 and its ligand podoplanin in vascular biology
Authors: Suzuki-Inoue Katsue , Tsukiji Nagaharu 
Published: February 2024

Purpose of review
Platelets are essential for hemostasis and are also vital in lymphatic and lung development and the maintenance of vascular integrity. Platelet activation receptor C-type lectin-like receptor 2 (CLEC-2) and its endogenous ligand podoplanin (PDPN) in lymphatic endothelial cells (LECs) and other cells regulate these processes. This review aims to comprehensively summarize the roles of platelet CLEC-2 and PDPN. This review also focuses on discussing the underlying mechanisms by which platelet CLEC-2 and PDPN mediate blood/lymphatic separation.

Findings
CLEC-2/PDPN-induced platelet activation in the primary lymph sacs, developmental lymphovenous junctions, neonatal mesentery, and the site of tumor lymphangiogenesis prevents blood/lymphatic vessel misconnection. Further, CLEC-2/PDPN-induced platelet activation is essential for lung development. Mice deficient in CLEC-2 or PDPN show blood-filled lymphatics, lung malformations, and cerebrovascular abnormalities. CLEC-2 deletion in steady-state adult mice did not result in blood/lymphatic vessel mixing. In adulthood, CLEC-2 maintains vascular integrity and that of high endothelial venules in lymph nodes. CLEC-2 deletion in adulthood results in hemorrhage under inflammatory conditions, and hemolymph nodes.

Summary
The platelet CLEC-2/LEC PDPN interaction prevents blood/lymphatic vessel mixing at active remodeling sites of the blood/lymphatic system, but not in steady-state adult mice. This interaction also regulates vascular integrity when vascular permeability increases before and after birth.
Costochondritis syndrome and thoracic-chest related pain: a scoping review
Authors: Bolandrini Andrea , Totti Vittoria , Segat Marco , Zaninetti Martina , Fascia Matteo , Segat Andrea , Minetti Federico , Margelli Michele , Maselli Filippo , Galeoto Giovanni 
Published: February 2024

ABSTRACTBackgroundCostochondritis is a frequent diagnosis related to chest pain but the etiology, treatment, and evolution of the disease are poorly documented.Clinical examination lacks specificity and most treatment recommendations are conservative in nature and have been traditionally accepted, perhaps because of the self-limited nature of the condition.However, costochondritis that does not self-resolve is referred to as atypical costochondritis and is associated with high medical expenses and psychological burden on the patient.This scoping review will aim to provide a clear overview about costochondritis, including definitions and terms, signs and symptoms, causes, diagnosis, treatment and prognosis. This work will also aim to propose shareable terms to describe this condition.Inclusion CriteriaEvery study describing a condition of non-cardiac musculoskeletal chest pain due to inflammation of the costochondral junctions of ribs or costosternal joints where the areas of tenderness are not generally accompanied by heat, erythema or localized swelling (e.g.,Tietze syndrome). This scoping review will consider studies conducted in any context. Articles in English or Italian will be considered.MethodsThe proposed scoping review will be conducted in accordance with the Joanna Briggs Institute methodology (JBI) for scoping reviews.The search will be carried out on 5 databases: MEDLINE, Embase, Cochrane Library, CENTRAL and CINAHL. Addictionally, research protocols will be searched on PROSPERO and ClinicalTrials.gov. Further research of grey literature will be carried out through OpenGrey and Google Scholar.Selection and data extraction will be conducted by two blind independent researchers and inconsistencies will be resolved by a third reviewer.The results will be presented in a schematic, tabular and descriptive format that will line up with the objectives and scope of the review.ConclusionsThis scoping review will aim to provide a comprehensive overview of the topic. The results will add meaningful information for clinicians. Furthermore, any knowledge gaps of the topic will be identified.
Quantitative genetics of naturalS. cerevisiaestrains upon sexual mating reveals heritable determinants of cellular fitness
Authors: Strauss Sivan Kaminski , Golomb Ruthie , Sheykhkarimli Dayag , Liti Gianni , Dahan Orna , Pilpel Yitzhak 
Published: February 2024

AbstractQuantitative genetics requires large datasets of diverse phenotyped-genotyped strains from the same species. A special need is for such archived biological material and computerized data in sexually reproducing individuals from a species. Here we leverage sexual mating among close to 100 diverse natural isolates of the yeastS. cerevisiaethat form about 4,000 offspring combinations in several ecologically relevant growth conditions. In a first genetic study of this new resource we focus on fitness measurements and its modes of inheritance as a quantitative trait from parents to offspring. We employ genomic barcoding of all strains and a barcode recombination technique to follow offspring of each successful mate combination. For all parents, and separately for all offspring we measure fitness under each condition. We focus on the inheritance of fitness, the ultimate evolutionary trait, and its inheritance as a quantitative trait upon sexual mating. Predicting offspring fitness given parental parameters is a major challenge as it is likely multi-factorial. We find that offspring fitness in fermentable carbon source correlates positively, yet modestly, with parental fitness, while on non-fermentable carbon, offspring fitness shows no detectable correlation with parental fitness. Instead, the non-fermentable condition, fitness of offspring increases sharply with genetic distance between their parents, suggesting that outbreeding maximizes offspring fitness irrespective of parental fitness at that condition. The number of minor alleles in the genome of each offspring, analogous to polygenic risk score in classical genetics, negatively correlates with offspring fitness in both conditions. Modeling of fitness inheritance shows that modes of inheritance are explained by either a dominance or a co-dominance models, in the fermentable and non-fermentable conditions respectively. Our newly suggested biological resource and data provide new foundations for a quantitative research in genetics and evolution upon sexual mating. Furthermore, our barcoded strains and mating tracking method provide an important research resource for the yeast community.
Discovery of a newMyristicaswamp in the Northern Western Ghats of India
Authors: Desai Pravin , Sadekar Vishal , Desai Shital 
Published: February 2024

AbstractMyristicaswamps are one of the world’s unique freshwater ecosystems. In recent years there has been an increase in the number of reports about their distribution along the western Ghats. In the current paper, we report a new distribution record for the occurrence ofMyristicaSwamp from the northern part of the western Ghats of Maharastra. TheMyristicaswamp is located within the Bhalandeshwar Sacred Grove of Kumbral Bagwadi, Dodamarg Maharastra, India. This forms a second report from the state of Maharastra. Frequent field visits were made to study and document the floral assemblage and biodiversity in the swamp from, November 2023 to January 2024. The swamp is dominated byMyristica magnificaBedd. The swamp is a part of a sacred grove and it is protected by Villagers due to religious beliefs. The discovery of this swamp points towards the possibility of the occurrence of more swamps in this region. Hence there is a need for a systematic survey for documenting swamps in the different areas.
Mapping Cell Fate Transition in Space and Time
Authors: Gu Yichen , Liu Jialin , Li Chen , Welch Joshua D. 
Published: February 2024

AbstractCell fate transition is fundamentally a spatiotemporal process, but previous work has largely neglected the spatial dimension. Incorporating both space and time into models of cell fate transition would be a key step toward characterizing how interactions among neighboring cells, the presence of local niche factors, and physical migration of cells contribute to tissue development. To realize this potential, we propose topological velocity inference (TopoVelo), a model for jointly inferring spatial and temporal dynamics of cell fate transition from spatial transcriptomic data. TopoVelo extends the RNA velocity framework to model single-cell gene expression dynamics of an entire tissue with spatially coupled differential equations. Our principled probabilistic approach enables the incorporation of time point labels and multiple slices. We further introduce the idea of cell velocity, which is defined as the physical direction of cell maturation and migration. Simulated data analysis indicates that incorporating spatial coordinates significantly improves the accuracy of velocity and time inference. When evaluated on real Slide-Seq and Stereo-Seq data, TopoVelo significantly improves the spatial coherence of inferred cell ordering compared to previous methods. Furthermore, TopoVelo accurately recovers the expected directions of cell differentiation and migration in the embryonic mouse cerebral cortex, gut, and lung. Our work introduces a new dimension into the study of cell fate transitions and lays a foundation for modeling the collective dynamics of cells comprising an entire tissue.