bluuebunny/crossref_metadata_2025_split huggingface dataset:
Severe cardiac and skeletal manifestations in DMD-edited microminipigs: an advanced surrogate for Duchenne muscular dystrophy
Authors: Otake Masayoshi , Imamura Michihiro , Enya Satoko , Kangawa Akihisa , Shibata Masatoshi , Ozaki Kinuyo , Kimura Koichi , Ono Etsuro , Aoki Yoshitsugu 
Published: May 2024

AbstractDuchenne muscular dystrophy (DMD) is an intractable X-linked muscular dystrophy caused by mutations in the DMD gene. While many animal models have been used to study the disease, translating findings to humans has been challenging. Microminipigs, with their pronounced physiological similarity to humans and notably compact size amongst pig models, could offer a more representative model for human diseases. Here, we accomplished precise DMD modification in microminipigs by co-injecting embryos with Cas9 protein and a single-guide RNA targeting exon 23 of DMD. The DMD-edited microminipigs exhibited pronounced clinical phenotypes, including perturbed locomotion and body-wide skeletal muscle weakness and atrophy, alongside augmented serum creatine kinase levels. Muscle weakness was observed as of one month of age, respiratory and cardiac dysfunctions emerged by the sixth month, and the maximum lifespan was 29.9 months. Histopathological evaluations confirmed dystrophin deficiency and pronounced dystrophic pathology in the skeletal and myocardial tissues, demonstrating that these animals are an unprecedented model for studying human DMD. The model stands as a distinct and crucial tool in biomedical research, offering deep understanding of disease progression and enhancing therapeutic assessments, with potential to influence forthcoming treatment approaches.
Synthetic phage-based approach for sensitive and specific detection of Escherichia coli O157
Authors: Tamura Azumi , Azam Aa Haeruman , Nakamura Tomohiro , Lee Kenichi , Iyoda Sunao , Kondo Kohei , Ojima Shinjiro , Chihara Kotaro , Yamashita Wakana , Cui Longzhu , Akeda Yukihiro , Watashi Koichi , Takahashi Yoshimasa , Yotsuyanagi Hiroshi , Kiga Kotaro 
Published: May 2024

AbstractEscherichia coli O157 can cause foodborne outbreaks, with infection leading to severe disease such as hemolytic-uremic syndrome. Although phage-based detection methods for E. coli O157 are being explored, research on their specificity with clinical isolates is lacking. Here, we describe an in vitro assembly-based synthesis of vB_Eco4M-7, an O157 antigen-specific phage with a 68-kb genome, and its use as a proof of concept for E. coli O157 detection. Linking the detection tag to the C-terminus of the tail fiber protein, gp27 produces the greatest detection sensitivity of the 20 insertions sites tested. The constructed phage detects all 53 diverse clinical isolates of E. coli O157, clearly distinguishing them from 35 clinical isolates of non-O157 Shiga toxin-producing E. coli. Our efficient phage synthesis methods can be applied to other pathogenic bacteria for a variety of applications, including phage-based detection and phage therapy.
Quantum sensing of microRNAs with nitrogen-vacancy centers in diamond
Authors: Zalieckas Justas , Greve Martin M. , Bellucci Luca , Sacco Giuseppe , Håkonsen Verner , Tozzini Valentina , Nifosì Riccardo 
Published: May 2024

AbstractLabel-free detection of nucleic acids such as microRNAs holds great potential for early diagnostics of various types of cancers. Measuring intrinsic biomolecular charge using methods based on field effect has been a promising way to accomplish label-free detection. However, the charges of biomolecules are screened by counter ions in solutions over a short distance (Debye length), thereby limiting the sensitivity of these methods. Here, we measure the intrinsic magnetic noise of paramagnetic counter ions, such as Mn2+, interacting with microRNAs using nitrogen-vacancy (NV) centers in diamond. All-atom molecular dynamics simulations show that microRNA interacts with the diamond surface resulting in excess accumulation of Mn ions and stronger magnetic noise. We confirm this prediction by observing an increase in spin relaxation contrast of the NV centers, indicating higher Mn2+ local concentration. This opens new possibilities for next-generation quantum sensing of charged biomolecules, overcoming limitations due to the Debye screening.
Vaccine effectiveness against emerging COVID-19 variants using digital health data
Authors: Varrelman Tanner J. , Rader Benjamin , Remmel Christopher , Tuli Gaurav , Han Aimee R. , Astley Christina M. , Brownstein John S. 
Published: May 2024

Abstract
Background
Participatory surveillance of self-reported symptoms and vaccination status can be used to supplement traditional public health surveillance and provide insights into vaccine effectiveness and changes in the symptoms produced by an infectious disease. The University of Maryland COVID Trends and Impact Survey provides an example of participatory surveillance that leveraged Facebook’s active user base to provide self-reported symptom and vaccination data in near real-time.

Methods
Here, we develop a methodology for identifying changes in vaccine effectiveness and COVID-19 symptomatology using the University of Maryland COVID Trends and Impact Survey data from three middle-income countries (Guatemala, Mexico, and South Africa). We implement conditional logistic regression to develop estimates of vaccine effectiveness conditioned on the prevalence of various definitions of self-reported COVID-like illness in lieu of confirmed diagnostic test results.

Results
We highlight a reduction in vaccine effectiveness during Omicron-dominated waves of infections when compared to periods dominated by the Delta variant (median change across COVID-like illness definitions: −0.40, IQR[−0.45, −0.35]. Further, we identify a shift in COVID-19 symptomatology towards upper respiratory type symptoms (i.e., cough and sore throat) during Omicron periods of infections. Stratifying COVID-like illness by the National Institutes of Health’s (NIH) description of mild and severe COVID-19 symptoms reveals a similar level of vaccine protection across different levels of COVID-19 severity during the Omicron period.

Conclusions
Participatory surveillance data alongside methodologies described in this study are particularly useful for resource-constrained settings where diagnostic testing results may be delayed or limited.
Cross‐talk reduction in metamaterial and non‐uniform transmission lines
Authors: Abbasi Hamid Reza , Rashed‐Mohassel Jalil A. , Moghadasi Mohammad Naser 
Published: May 2024

AbstractThe electromagnetic compatibility analysis of RF circuitry is essential due to the adverse effects on sensitive components. Two metamaterial unit cells with slow‐wave properties are presented for cross‐talk reduction in transmission lines. The analytical expressions for computing equivalent lumped elements of the lines are then provided. The dispersion diagram is obtained from the parameters extracted from the measurement. A microstrip as the generator line and five identical CRLH unit cells as the receptor line are then used and a significant reduction in cross‐talk is observed in comparison to conventional lines. A non‐uniform transmission line with two different CRLH unit cells as the receptor line is then employed and found effective in further cross‐talk reduction between the lines. The lengths of the lines and numbers of cells are kept the same in all lines for comparison. The simulated results are validated by measurements.
Abell 0399–Abell 0401 radio bridge spectral index: First multi-frequency detection
Authors: Pignataro G. V. , Bonafede A. , Bernardi G. , de Gasperin F. , Brunetti G. , Pasini T. , Vazza F. , Biava N. , de Jong J. M. G. H. J. , Cassano R. , Botteon A. , Brüggen M. , Röttgering H. J. A. , van Weeren R. J. , Shimwell T. W. 
Published: May 2024

Aims. Recent low-frequency radio observations at 140 MHz discovered a bridge of diffuse emission with a length of 3 Mpc that connects the galaxy clusters Abell 0399 and Abell 0401. We present follow-up observations at 60 MHz to constrain the spectral index of the bridge, which has only been detected at 140 and 144 MHz so far.
Methods. We analysed deep (∼18 h) LOw Frequency ARray (LOFAR) Low Band Antenna (LBA) data at 60 MHz to detect the bridge at very low frequencies. We then conducted a multi-frequency study with LOFAR HBA data at 144 MHz and uGMRT data at 400 MHz. Assuming second-order Fermi mechanisms for the re-acceleration of relativistic electrons driven by turbulence in the radio bridge regions, we compared the observed radio spectrum with theoretical synchrotron models.
Results. The bridge is detected in the 75″ resolution LOFAR image at 60 MHz, and its emission fully connects the region between the two galaxy clusters. Between 60 MHz and 144 MHz, we found an integrated spectral index value of α60144 = −1.44 ± 0.16 for the bridge emission. For the first time, we produced spectral index and related uncertainties maps for a radio bridge. We produce a radio spectrum that shows a significant steepening between 144 and 400 MHz.
Conclusions. This detection at low frequencies provides important information for models of particle acceleration and magnetic field structure on very extended scales. The spectral index gives important clues about the origin of inter-cluster diffuse emission. The steepening of the spectrum above 144 MHz can be explained in a turbulent re-acceleration framework, assuming that the acceleration timescales are longer than ∼200 Myr.
EOS software evolution enabling LHC Run 3
Authors: Caffy Cedric , Amadio Guilherme , Guenther Jaroslav , Lekshmanan Abhishek , Mascetti Luca , Peters Andreas , Reis Manuel , Simon Michal Kamil , Sindrilaru Elvin , Smith David 
Published: May 2024

EOS has been the main storage system at CERN for more than a decade, continuously improving in order to meet the ever evolving requirements of the LHC experiments and the whole physics user community. In order to satisfy the demands of LHC Run-3, in terms of storage performance and tradeoff between cost and capacity, EOS was enhanced with a set of new functionalities and features that we will detail in this paper.
First of all, we describe the use of erasure coded layouts in a large-scale deployment which enables an efficient use of available storage capacity, while at the same time providing end-users with better throughput when accessing their data. This new operating model implies more coupling between the machines in a cluster, which in turn leads to the next set of EOS improvements that we discuss, targeting I/O traffic shaping, better I/O scheduling policies and tagged traffic prioritization. Increasing the size of the EOS clusters to cope with experiment demands, means stringent constraints on the data integrity and durability that we addressed by a re-designed consistency check engine. Another focus area of EOS development was to minimize the operational load by making the internal operational procedures (draining, balancing or conversions) more robust and efficient, to allow managing easily multiple clusters and avoid possible scaling issues.
All these improvements available in the EOS 5 release series, are coupled with the new XRootD 5 framework which brings additional security features like TLS support and optimizations for large data transfers like page read and page write functionalities. Last but not least, the area of authentication/authorization methods has seen important developments by adding support for different types of bearer tokens that we will describe along with EOS specific token extensions. We conclude by highlighting potential areas of the EOS architecture that might require further developments or re-design in order to cope with the ever-increasing demands of our end-users.
Multidatabase The Future of the data storage in Particle Physics and Astronomy
Authors: Hřivnáč Julius , Peloton Julien 
Published: May 2024

Particle Physics experiments and Astronomy telescopes store alarge amount of data, most of those data are usually stored in simple files in various formats. Databases are used only to a limited extend, while database technology has made a tremendous progress in recent years, offering a large spectrum of applications in all possible domains. Those possibilities are still largely underused.The article demonstrates the data architecture transparently using multiple database types, namely SQL database, NoSQL database and Graph database. Each database is used for the domain where it is the most appropriate and the cross-technology access is offered to users. The strong and weak points of all three technologies are discussed. Several possible ways of organizing interactionbetweendatabases aredescribed.The architecture is illustrated on the concrete implementation of the data storage oftheFinkproject, usingJanusGraph andHBasetechnologiesto store alerts from theRubinObservatory. HBaseis used to store thebulkdata and the structuralinformationis storedinGraphs, allowing transparent access to alldata and deep analyses of relationbetween alerts and other objects. Ways for implementing heterogeneous database architecture in general HEP applications are outlined.
Operation of the CERN disk storage infrastructure during LHC Run-3
Authors: Caffy Cedric , Amadio Guilherme , Arsuaga Rios Maria , Batalha Reis Manuel , Capitoni Niccolo , Contescu Cristian , Guenther Jaroslav , Mascetti Luca , Peters Andreas , Sindrilaru Elvin , Vrachnaki Ioanna , Lekshmanan Abhishek 
Published: May 2024

The CERN IT Storage group operates multiple distributed storage systems to support all CERN data storage requirements. The storage and distribution of physics data generated by LHC and non-LHC experiments is one of the biggest challenges the group has to take on during LHC Run-3.EOS [1], the CERN distributed disk storage system is playing a key role in LHC data-taking. During the first ten months of 2022, more than 440PB have been written by the experiments and 2.9EB have been read out. The data storage requirements of LHC Run-3 are higher than what was previously delivered. The storage operations team has started investigating multiple areas to upgrade and optimize the current storage resources. A new, dedicated and redundant EOS infrastructure based on 100Gbit servers was installed, commissioned and deployed for the ALICE Online and Offline (O2) project. This cluster can sustain high-throughput data transfer between the ALICE Event Processing Nodes (EPN) and the CERN’s data center.This paper will present the architecture, techniques and workflows in place allowing EOS to deliver fast, reliable and scalable data storage to meet experiment needs during LHC Run-3 and beyond.
A High-Speed Asynchronous Data I/O Method for HEPS
Authors: Fu Shiyuan , Wang Lu , Cheng Yaodong , Hu Yu , Liu Rui , Wang Lei , Wang Shuang , Liu Jianli , Sun Haokai , Qi Fazhi 
Published: May 2024

The High Energy Photon Source (HEPS) is expected to produce a substantial volume of data, lead to immense data I/O pressure during computing. Inefficient data I/O can significantly impact computing performance.
To address this challenge, firstly, we have developed a data I/O framework for HEPS. This framework consists of three layers: data channel layer, distributed memory management layer, and I/O interface layer. It mask the underlying data differences in formats and sources, while implementing efficient I/O methods. Additionally, it supports both stream computing and batch computing.
Secondly, we have designed a data processing pipeline scheme aimed at reducing I/O latency and optimizing I/O bandwidth utilization during the processing of high-throughput data. This involves breaking down the computing task into several stages, including data loading, data pre-processing, data processing, and data writing, which are executed asynchronously and in parallel.
Finally, we introduce the design of stream data I/O process. The primary objective of stream data I/O is to enable real-time online processing of raw data, avoiding I/O bottlenecks caused by disk storage. This approach ensures the stability of data transmission and integrates distributed memory management to guarantee data integrity in memory.
Controlling Quality for a Physics-Driven Generative Models and Auxiliary Regression Approach
Authors: Rogachev Alexander , Ratnikov Fedor 
Published: May 2024

High energy physics experiments heavily rely on the results of MC simulation of data used to extract physics results. However, the detailed simulation often requires tremendous amount of computation resources.
Using Generative Adversarial Networks and other deep learning generative techniques can drastically speed up the computationally heavy simulations like a simulation of the calorimeter response. To be useful, such models are required to satisfy quality metrics which are driven by a specific physics properties of generated objects rather than by a regular ML image-like quality metrics.
The auxiliary regression extension to the GAN-based fast simulation demonstrated improvements of the physics quality for generated objects. This approach introduces physics metrics to a Discriminator path of the model thus allows direct discriminating of objects with poorly reproduced properties.
In this paper we discuss the auxiliary regression GAN approach to physicsbased fast simulation and concentrate on requirements to the quality of the auxiliary regressor to provide a necessary precision of the generative models built on top of this regressor.
Adjunctive bevacizumab therapy in an equine corneal stromal invasive
squamous cell carcinoma with a 53-months follow-up
Authors: Blohm Klaas-Ole , Nell Barbara 
Published: May 2024

AbstractA 17-year-old Appaloosa mare was referred for evaluation of presumed refractory
keratitis of the left eye. Gross examination revealed ocular discomfort and
corneal neovascularization with a nasal focal opacification affecting
approximately 40% of the corneal surface. On ophthalmic examination, extensive
subepithelial to mid-stromal vascular branching accompanied by a homogeneous
white, dense opacification, which affected up to 80% of the total corneal
thickness, were apparent. Signs of concurrent uveitis were absent. Deep-stromal
lamellar keratectomy with a conjunctival pedicle graft was performed under
general anesthesia. Histopathology confirmed a poorly differentiated corneal
stromal invasive squamous cell carcinoma (SI-SCC) with neoplastic cell extension
to the surgical margins. Postoperatively, 4 topical mitomycin C 0.04%
chemotherapy cycles combined with oral firocoxib therapy were initiated. Seven
months after surgery, regrowth of the SI-SCC was clinically suspected. A total
volume of 1 ml bevacizumab 2.5% was administered in the standing sedated horse
via 3 mid-stromal corneal injections. Four weeks later, intrastromal bevacizumab
injections (ISBIs) were repeated, however, this time the solution was injected
directly into the main corneal vessel branches.Seven weeks after the second ISBIs, the left eye was comfortable and significant
remission of corneal vascularization and opacity was recognized. No recurrence
has been noted for a follow-up period of more than 53 months.Equine SI-SCC usually has a very poor prognosis for globe maintenance. To the
authors’ knowledge this is the first report of well-tolerated intrastromal
antivascular endothelial growth factor adjunctive therapy with bevazicumab 2.5%
and SI-SCC resolution after a multimodal treatment approach.
Individueller Konzentrationsverlauf von Progesteron und Östradiol-17β
im Blut bei Stuten während des Zyklus
Authors: Laufkötter Sara , Längerer Lina , Wehrend Axel 
Published: May 2024

Zusammenfassung
Gegenstand und Ziel Die Studie stellt den individuellen Verlauf der
Konzentrationen von Östradiol-17ß und Progesteron im Blut von Stuten über einen
Zyklus dar, um auf physiologische individuelle Unterschiede zwischen einzelnen
Tieren hinzuweisen und Interpretationshilfen von Hormonwerten zu geben.
Material und Methoden An 7 Stuten wurde über den Zyklusverlauf die
Konzentrationen an Progesteron und Östradiol-17ß bestimmt. Eine Stute wurde
aufgrund eines vom physiologischen Zyklus abweichenden Verlaufs aus der
Beurteilung ausgeschlossen. Zusätzlich wurden die Ovarien täglich sonografisch
untersucht, um die Hormonwerte morphologischen Veränderungen auf den Ovarien
zuordnen zu können.
Ergebnisse Teilweise zeigen Stuten erhebliche individuelle Unterschiede in
ihren Hormonverläufen, die sich auch von den veröffentlichten Vergleichswerten
in der Literatur unterscheiden. So zeigten 2 Stuten zum Zeitpunkt der Ovulation
einen Progesteronwert oberhalb des Basalniveaus. Die postovulatorischen
Progesteronverläufe der Stuten zeigen deutliche Schwankungen, was die Angabe von
Referenzwerten in den verschiedenen Abschnitten der Gelbkörperphase erschwert.
Die Länge der Plateauphasen beträgt im Durchschnitt 12,3±1,5 Tage. Die Stute mit
der Doppelovulation zeigte die höchsten Progesteronkonzentrationen.
Schussfolgerung Die Messung von Plasmaprogesteronwerten bei Stuten sollten
nur im Zusammenhang mit weiteren Untersuchungsergebnissen interpretiert werden.
Die sehr starken Schwankungen der Östradiol-17ß-Konzentrationen machen es
fraglich, ob die Bestimmung dieses Hormonwertes einen diagnostischen Nutzen
hat.
Klinische Relevanz Bei der Interpretation von Steroidhormonwerten im
ingraviden Zyklus einer Stute sind die individuellen Verläufe zu beachten, die
teilweise deutlich von den veröffentlichten Referenzwerten abweichen.
Diagnose und Therapie eines persistierenden Ductus arteriosus: Eine
retrospektive Evaluation bei 17 Katzen
Authors: Masche Anja , Breit Peter , Höpfner Robert , Schmerbach Kay 
Published: May 2024

Zusammenfassung
Gegenstand und Ziel Ziel der Studie war die Darstellung des Signalements,
der klinischen Merkmale und echokardiographischen Ergebnisse von Katzen, die
wegen eines persistierenden Ductus arteriosus (PDA) behandelt wurden sowie der
kurz- bis mittelfristigen Ergebnisse nach erfolgreicher Ligatur des PDA.
Material und Methoden Die Studie ist eine retrospektive Untersuchung von
17 Katzen mit einem PDA über einen Zeitraum von 10 Jahren. Die Diagnosestellung
PDA erfolgte mittels transthorakaler Echokardiografie. Es wurden 13 Katzen
chirurgisch mittels Thorakotomie und Ligatur des PDA versorgt.
Ergebnisse Bei allen Katzen wurde ein Herzgeräusch festgestellt, welches
sich größtenteils mit einer Lautstärke von Grad 4 bis 6 zeigte (15/17 Katzen;
88,2%). Ein kontinuierliches Herzgeräusch trat häufiger auf (10/17 Katzen;
58,9%) als ein systolisches (7/17 Katzen; 41,1%). Echokardiografisch zeigten
sich bei der Mehrheit der Katzen der linksventrikuläre enddiastolische
Durchmesser (LVIDd) sowie der linksventrikuläre endsystolische Durchmesser
(LVIDs) deutlich über den Referenzwerten. Der Durchmesser des PDA (gemessen an
der breitesten Stelle des Gefäßes) lag im Mittel bei 3,4 mm±1,08 mm und die
mediane maximale Durchflussgeschwindigkeit bei 5,06 m/sek (2,6m/sek–6,4m/sek).
Bei allen chirurgisch versorgten Katzen wurde die Operation erfolgreich
abgeschlossen und alle Katzen wurden nach anschließender stationärer Therapie
entlassen. Bei einer Katze kam es perioperativ zu einer Blutung aus dem PDA, die
gestillt werden konnte. Diese Katze zeigte postoperativ einen Restshunt, welcher
in einer Kontrollechokardiografie 3 Monate später nicht mehr dargestellt werden
konnte. Sechs Katzen konnten über einen längeren Zeitraum verfolgt werden.
Schlussfolgerungen Mit einer postoperativen Überlebensrate von 100% liegt
in dieser Studie eine sehr gute chirurgische Prognose vor.
Klinische Relevanz Die chirurgische Behandlung des PDA ist bei Tieren ohne
fortgeschrittene Herzveränderungen kurativ. Erste Hinweise kann die Auskultation
eines Herzgeräusches geben. Zwar ist die erste klinische Diagnostik mit der
Auskultation einfach und sollte bei jeder Erstvorstellung bereits im jungen
Alter erfolgen, jedoch muss bedacht werden, dass nicht jede Katze mit PDA ein
kontinuierliches Herzgeräusch zeigen muss. Hierbei sollten vor allem die
klinischen Symptome berücksichtigt werden.