bluuebunny/crossref_metadata_2025_split huggingface dataset:
(316) ASSESSMENT OF ERECTILE DYSFUNCTION AND PEYRONIE DISEASE: A STUDY USING THE ERECTION HARDNESS SCORE AND LIEF QUESTIONNAIRE
Authors: Rocha Chavez Zambrana D , Cambuí Castro Lima G , Fonseca Ribeiro JV , Souza JH , Barbosa Garofo Stabile Moura D , Lazzarini Marani A , Miolaro De Mello LG , Fonseca Moreira W , Noffs S , Lemos C , Nardozza Junior A , Brandão Vasco M , De Souza Carneiro MP 
Published: December 2024

Abstract

Introduction
Erectile dysfunction (ED) and Peyronie’s disease (PD) are common conditions that affect men’s sexual health. Erectile dysfunction may manifest as a subsequent symptom in Peyronie’s disease, occurring in 30-70.6% of patients, due to the formation of fibrotic plaques in the tunica albuginea, along with penile shortening and deformity. Consequently, it is essential to evaluate these conditions using validated clinical scales that are straight forward to administer.

Objective
To assess the severity of erectile dysfunction and the erection hardness score in men with erectile dysfunction only and erectile dysfunction coexisting with Peyronie’s disease.

Methods
A cross-sectional study investigation involving male patients diagnosed with Erectile Dysfunction and Peyronie’s Disease. We selected patients with surgical indications for PD and those with ED unresponsive to oral medication therapy. The International Index of Erectile Function (IIEF-15) questionnaire was administered to assess sexual function. Additionally, we evaluated the Erection Hardness Score (EHS) in patients who underwent penile Doppler Ultrasound with pharmacological induction 15 minutes after medication application. All statistical analyses were conducted using RStudio and we performed Pearson’s chi-squared test with a significance level of p &lt; 0.05.

Results
We evaluated 135 men from January 2022 to April 2024. The participant has a mean age of 61.44 ± 9.6 years. The results stratified by IIEF, Erectile Dysfunction (ED) vs. ED with Peyronie’s Disease (ED + PD): Mild ED: 3.5% vs. 14.3%; Mild to Moderate ED: 7.0% vs.14.3%; Moderate ED: 12.8% vs. 26.5%; Severe ED: 73.3% vs. 32.7%; No ED: 3.5% vs. 12.2%. The EHS demonstrated an average ED 2.41 ± 1.09 and ED + PD 3.29 ± 0.87. The chi-square test indicates significant association between IIEF score with DE vs ED + PD (p &lt; 0.001) and between the EHS with ED vs ED + PD (p &lt; 0.001).

Conclusions
The severity of erectile dysfunction according to the IIEF and the degree of erection according to the EHS are associated with the type of erectile dysfunction - ED only or erectile dysfunction with Peyronie’s disease.

Disclosure
No.
Floret development and fertility of barley as affected by Photoperiod-H1 under contrasting photoperiods and PHYTOCHROME C backgrounds
Authors: Parrado Jorge D , Savin Roxana , Slafer Gustavo A 
Published: December 2024

Abstract
The photoperiod-insensitive allele of Photoperiod-H1 (ppd-H1) increases spike fertility in barley, both indirectly by lengthening flowering time and directly when flowering time is accelerated under extra long photoperiods. To determine if the effect of PPD-H1 on spike fertility is related to the initiation or the mortality of spikelets/florets, we performed detailed analysis of the dynamics of floret development along the barley spikes. Four near-isogenic lines (NILs) combining ppd-H1 and Ppd-H1 alleles with two PHYTOCHROME C (PhyC-l and PhyC-e) backgrounds were compared under 12 h and 24 h photoperiods. The ppd-H1 line consistently showed higher survival rates of floret primordia. Fertility differences were observed within spikes, with the insensitive ppd-H1 line improving fertility in the less favoured distal florets, and even inducing more developmental progress before floret mortality in apical spikelets. The ppd-H1 allele constitutively enhanced floret primordia survival, as the effect was seen even under long photoperiods when lines had similar phenology. The dynamics of floret development affecting spike fertility resulted in a parallel effect on grain setting. Together, these results indicate that photoperiod insensitivity in barley contributes to greater yield potential by reducing floret primordia mortality and improving spike fertility.
The Epilepsy Centers of Excellence at the Veterans Health Administration
Authors: Haneef Zulfi , Casanova Caleb A , Zhang Vincent , Bonds King Jennifer R , Rehman Rizwana , Garga Nina I , Graham Glenn D , Towne Alan R 
Published: December 2024

ABSTRACT

Introduction
The Veterans Health Administration (VHA) Epilepsy Centers of Excellence (ECoE) was established in 2008 to provide specialized care for veterans with epilepsy. Although established more than a decade ago, there has been no systematic evaluation of the ECoE’s performance in key mission areas. We evaluated their performance in several key mission areas—clinical care, research, education, and outreach—since inception to evaluate their success in meeting the initial mandate.

Materials and Methods
We analyzed available data from relevant literature, ECoE annual reports, and the ECoE website between 2011 and 2023. Clinical care is the primary mission of the ECoE and was evaluated by examining utilization data for various clinical services and published literature. Research was assessed based on academic output and funding reported in the annual reports. Education and outreach were qualitatively assessed using recent data on the ECoE website and annual reports.

Results
Total unique patient clinical visits for therapeutic/diagnostic encounters increased by 74% (from 10,487 in 2011 to 18,285 in 2023), which was nearly twice the 39.5% growth in workforce strength (from 119 in 2011 to 166 in 2022) over a similar period. Care provided by the ECoE is associated with decreased mortality rates compared to patients who do not receive ECoE neurology care. Tele-epilepsy visits increased considerably following the COVID-19 pandemic, from 1,928 in 2019 to 4,950 in 2021 (a 157% increase over 2 years). Research grant funding in fiscal year 2023 totaled approximately $4 million for ECoE-affiliated investigators. Outreach efforts included several VHA/non-VHA collaborations. The ECoE organizational structure was found to be highly interconnected and regionally represented, with special committees devoted to many key mission areas of epilepsy care.

Conclusions
Our analysis reveals progressive growth and improvements in the ECoE mission areas of clinical care, research, education, and outreach. Clinical utilization data have shown growth since inception, while also leading to lower mortality rates and lower costs per patient, fulfilling the organizational mandate to improve the care of veterans with epilepsy. There is substantial activity in research, education, and outreach. The ECoE governance hierarchy aims to facilitate smooth resource allocation both regionally and for the key mission areas. Our findings can help policymakers assess and prioritize future ECoE initiatives, while other clinical care organizations can seek to model their care based on the ECoE.
Mpox (Monkeypox) On Board a Naval Warship
Authors: López Lourdes M , Newkirk Russell E , McAuliffe Liane , Bloomquist Luke , Zenilman Jonathan M 
Published: December 2024

ABSTRACT
We report a case of mpox in an active duty male on board a naval warship, who presented with a chancre-like penile lesion and ulcerating lymphadenopathy in the setting of a nonreactive treponemal test. Despite empirical therapy for sexually transmitted infections, he developed a fever and a generalized pustular rash. The patient was placed in isolation, and contact tracing was performed. No further spread of mpox was identified despite close contact with multiple shipmates and a pet rabbit. This case highlights the obligation of medical providers who care for our military personnel and veterans to offer JYNNEOS vaccine to high-risk individuals. Additionally, with the rise in clade I mpox cases prompting a recent global health emergency declaration by the World Health Organization, it is essential to implement proper testing methods and treatments when considering mpox in the differential diagnosis because of its association with other sexually transmitted infections.
3D gap opening in non-ideal MHD protoplanetary discs: asymmetric accretion, meridional vortices, and observational signatures
Authors: Hu Xiao , Li Zhi-Yun , Bae Jaehan , Zhu Zhaohuan 
Published: December 2024

ABSTRACT
Recent high angular resolution ALMA observations have revealed rich information about protoplanetary discs, including ubiquitous substructures and three-dimensional gas kinematics at different emission layers. One interpretation of these observations is embedded planets. Previous 3D planet–disc interaction studies are either based on viscous simulations or non-ideal magnetohydrodynamics (MHD) simulations with simple prescribed magnetic diffusivities. This study investigates the dynamics of gap formation in 3D non-ideal MHD discs using non-ideal MHD coefficients from the look-up table that is self-consistently calculated based on the thermochemical code. We find a concentration of the poloidal magnetic flux in the planet-opened gap (in agreement with previous work) and enhanced field-matter coupling due to gas depletion, which together enable efficient magnetic braking of the gap material, driving a fast accretion layer significantly displaced from the disc mid-plane. The fast accretion helps deplete the gap further and is expected to negatively impact the planet growth. It also affects the corotation torque by shrinking the region of horseshoe orbits on the trailing side of the planet. Together with the magnetically driven disc wind, the fast accretion layer generates a large, persistent meridional vortex in the gap, which breaks the mirror symmetry of gas kinematics between the top and bottom disc surfaces. Finally, by studying the kinematics at the emission surfaces, we discuss the implications of planets in realistic non-ideal MHD discs on kinematics observations.
Spider-Webb: JWST Near Infrared Camera resolved galaxy star formation and nuclear activities in the Spiderweb protocluster at z = 2.16
Authors: Shimakawa Rhythm , Koyama Yusei , Kodama Tadayuki , Dannerbauer Helmut , Pérez-Martínez J M , Röttgering Huub J A , Tanaka Ichi , D’Eugenio Chiara , Naufal Abdurrahman , Daikuhara Kazuki , Zhang Yuheng 
Published: December 2024

ABSTRACT
Near-infrared (NIR) emission is less affected by dust than ultraviolet and optical emission and is therefore useful for studying the properties of dust-obscured galaxies. Although rest-frame NIR observations of high-redshift galaxies have long been made using space telescopes, their structures were unresolved due to the lack of angular resolution. This letter reports the early results from the analysis of high-resolution Pa$\beta$ imaging of the Spiderweb protocluster at $z=2.16$ with the JWST Near Infrared Camera. We investigate radial profiles of Pa$\beta$ lines and rest-frame NIR continua from luminous H $\alpha$-emitting galaxies (HAEs) in the protocluster. Particularly, we compare those of 11 HAEs (N-HAEs) on the star-forming main sequence with those of 8 HAEs (X-HAEs) with X-ray active galactic nuclei (AGNs). Resultant composite Pa$\beta$ line images of N-HAEs indicate significant star formation in galactic discs. In contrast, X-HAEs are dominated by point source components rather than outer star formation, as inferred from our earlier work based on multiwavelength spectral energy distribution fitting. Given their higher stellar potentials suggested from their rest-frame NIR images, the different characteristics may be driven by the impact of AGN feedback.
The sensory shark: high-quality morphological, genomic and transcriptomic data for the small-spotted catshark Scyliorhinus canicula reveal the molecular bases of sensory organ evolution in jawed vertebrates
Authors: Mayeur H , Leyhr J , Mulley J , Leurs N , Michel L , Sharma K , Lagadec R , Aury J -M , Osborne O G , Mulhair P , Poulain J , Mangenot S , Mead D , Smith M , Corton C , Olive K , Skelton J , Betteridge E , Dolucan J , Dudchenko O , Omer A D , Weisz D , Aiden E L , McCarthy S , Sims Y , Torrance J , Tracey A , Howe K , Baril T , Hayward A , Martinand-Mari C , Sanchez S , Haitina T , Martin K , Korsching S I , Mazan S , Debiais-Thibaud M 
Published: December 2024

Abstract
Cartilaginous fishes (chondrichthyans: chimaeras and elasmobranchs -sharks, skates and rays) hold a key phylogenetic position to explore the origin and diversifications of jawed vertebrates. Here, we report and integrate reference genomic, transcriptomic and morphological data in the small-spotted catshark Scyliorhinus canicula to shed light on the evolution of sensory organs. We first characterise general aspects of the catshark genome, confirming the high conservation of genome organisation across cartilaginous fishes, and investigate population genomic signatures. Taking advantage of a dense sampling of transcriptomic data, we also identify gene signatures for all major organs, including chondrichthyan specializations, and evaluate expression diversifications between paralogs within major gene families involved in sensory functions. Finally, we combine these data with 3D synchrotron imaging and in situ gene expression analyses to explore chondrichthyan-specific traits and more general evolutionary trends of sensory systems. This approach brings to light, among others, novel markers of the ampullae of Lorenzini electro-sensory cells, a duplication hotspot for crystallin genes conserved in jawed vertebrates, and a new metazoan clade of the transient-receptor potential (TRP) family. These resources and results, obtained in an experimentally tractable chondrichthyan model, open new avenues to integrate multiomics analyses for the study of elasmobranchs and jawed vertebrates.
Muscle vasculitis in patients with polymyalgia rheumatica: Three case series
Authors: Moriya Haruka , Fujieda Yuichiro , Inoue Yuta , Miyamoto Kenichi , Anada Mamiko , Tanaka Daiki , Kudo Akihiko , Abe Megumi , Nagai Azusa , Hisada Ryo , Kono Michihito , Kato Masaru , Amengual Olga , Matsuno Yoshihiro , Yabe Ichiro , Atsumi Tatsuya 
Published: December 2024

ABSTRACT
Polymyalgia rheumatica (PMR) is a common inflammatory disorder characterized by myalgia/stiffness in proximal hip and shoulder girdle, elevated C reactive protein, and erythrocyte sedimentation rate, but its pathogenesis is not fully elucidated. We report three cases of PMR who do not respond adequately to standard treatment. Those patients had typical symptoms of myalgia and muscle weakness, with elevated C reactive protein in absence of creatine kinase elevation. Muscle specimen showed the findings of vasculitis in all cases; therefore, muscular-limited vasculitis may be an underlying pathology in PMR in those refractory cases.
Writing (Re)Considered
Authors: Barna Alyssa 
Published: December 2024

Abstract
Writing is the currency of our academic life as music theorists. Scholars entering the field are expected to demonstrate fluency in writing in order to participate in music-theoretical discourse. Inspired by my written work as a Public Music Theorist, I reconsider how writing is taught and assessed at various levels. Through an examination of literature on writing, music theory pedagogy, and Public Music Theory, I present my philosophy of writing along with recommendations for improving clarity and mentorship for writers. This article asks two questions: What can we learn from Public Music Theory to communicate our ideas more clearly in writing, promote inclusivity, and expand the definition of music theory? And who holds the power to make change within our written discourse and training?
Accurate quantification of nascent and mature RNAs from single-cell and single-nucleus RNA-seq
Authors: Sullivan Delaney K , Hjörleifsson Kristján Eldjárn , Swarna Nikhila P , Oakes Conrad , Holley Guillaume , Melsted Páll , Pachter Lior 
Published: December 2024

Abstract
In single-cell and single-nucleus RNA sequencing (RNA-seq), the coexistence of nascent (unprocessed) and mature (processed) messenger RNA (mRNA) poses challenges in accurate read mapping and the interpretation of count matrices. The traditional transcriptome reference, defining the “region of interest” in bulk RNA-seq, restricts its focus to mature mRNA transcripts. This restriction leads to two problems: reads originating outside of the “region of interest” are prone to mismapping within this region, and additionally, such external reads cannot be matched to specific transcript targets. Expanding the “region of interest” to encompass both nascent and mature mRNA transcript targets provides a more comprehensive framework for RNA-seq analysis. Here, we introduce the concept of distinguishing flanking k-mers (DFKs) to improve mapping of sequencing reads. We have developed an algorithm to identify DFKs, which serve as a sophisticated “background filter”, enhancing the accuracy of mRNA quantification. This dual strategy of an expanded region of interest coupled with the use of DFKs enhances the precision in quantifying both mature and nascent mRNA molecules, as well as in delineating reads of ambiguous status.
QClus: a droplet filtering algorithm for enhanced snRNA-seq data quality in challenging samples
Authors: Schmauch Eloi , Ojanen Johannes , Galani Kyriakitsa , Jalkanen Juho , Harju Kristiina , Hollmén Maija , Kokki Hannu , Gunn Jarmo , Halonen Jari , Hartikainen Juha , Kiviniemi Tuomas , Tavi Pasi , Kaikkonen Minna U , Kellis Manolis , Linna-Kuosmanen Suvi 
Published: December 2024

Abstract
Single-nuclei RNA sequencing remains a challenge for many human tissues, as incomplete removal of background signal masks cell-type-specific signals and interferes with downstream analyses. Here, we present Quality Clustering (QClus), a droplet filtering algorithm targeted toward challenging samples. QClus uses additional metrics, such as cell-type-specific marker gene expression, to cluster nuclei and filter empty and highly contaminated droplets, providing reliable filtering of samples with varying number of nuclei and contamination levels. In a benchmarking analysis against seven alternative methods across six datasets, consisting of 252 samples and over 1.9 million nuclei, QClus achieved the highest quality in the greatest number of samples over all evaluated quality metrics and recorded no processing failures, while robustly retaining numbers of nuclei within the expected range. QClus combines high quality, automation and robustness with flexibility and user-adjustability, catering to diverse experimental needs and datasets.
Degradation and stable maintenance of adeno-associated virus inverted terminal repeats in E. coli
Authors: Radukic Marco T , Le Dinh To , Krassuski Timo , Borchert Philipp , Leach David R F , Müller Kristian M 
Published: December 2024

Abstract
Current plasmid propagation in E. coli compromises large inverted repeats, such as inverted terminal repeats (ITRs) of adeno-associated virus (AAV). Direct long-read sequencing analyses upon varying strains and culture conditions revealed ITR instability caused by a slipped misalignment mechanism, although other mechanism probably contribute. ITRs stabilized in absence of SbcC, which is part of the SbcCD nuclease complex, a human Mre11–Rad50 homolog, or at elevated growth temperatures (e.g. 42°C), with a combination being optimal. Resulting full ITR transgene plasmids improved rAAV yield and purity in HEK-293 productions. The findings advance plasmid biology, cloneable sequences and therapeutic AAV manufacturing.
AnnoGCD: a generalized category discovery framework for automatic cell type annotation
Authors: Ceccarelli Francesco , Liò Pietro , Holden Sean B 
Published: December 2024

Abstract
The identification of cell types in single-cell RNA sequencing (scRNA-seq) data is a critical task in understanding complex biological systems. Traditional supervised machine learning methods rely on large, well-labeled datasets, which are often impractical to obtain in open-world scenarios due to budget constraints and incomplete information. To address these challenges, we propose a novel computational framework, named AnnoGCD, building on Generalized Category Discovery (GCD) and Anomaly Detection (AD) for automatic cell type annotation. Our semi-supervised method combines labeled and unlabeled data to accurately classify known cell types and to discover novel ones, even in imbalanced datasets. AnnoGCD includes a semi-supervised block to first classify known cell types, followed by an unsupervised block aimed at identifying and clustering novel cell types. We evaluated our approach on five human scRNA-seq datasets and a mouse model atlas, demonstrating superior performance in both known and novel cell type identification compared to existing methods. Our model also exhibited robustness in datasets with significant class imbalance. The results suggest that AnnoGCD is a powerful tool for the automatic annotation of cell types in scRNA-seq data, providing a scalable solution for biological research and clinical applications. Our code and the datasets used for evaluations are publicly available on GitHub: https://github.com/cecca46/AnnoGCD/.
The soluble guanylate cyclase activator runcaciguat significantly improves albuminuria in patients with chronic kidney disease: a randomized placebo-controlled clinical trial
Authors: Gansevoort Ron T , Wheeler David C , Debén Francisco Martínez , Speeckaert Marijn , Thomas Dirk , Berger Mario , Klein Stefan , Friedrichs Frauke , Paraschin Karen , Schmieder Roland E 
Published: December 2024

ABSTRACT

Background and hypothesis
In chronic kidney disease (CKD) the nitric oxide (NO)−soluble guanylate cyclase (sGC)−cyclic guanosine monophosphate (cGMP) pathway is impaired. Runcaciguat, an sGC activator, activates heme-free sGC, restoring cGMP production. This phase 2a trial studied the efficacy, safety, and tolerability of runcaciguat in CKD patients with or without sodium-glucose co-transporter-2 inhibitor (SGLT2i).

Methods
Patients with CKD and established atherosclerotic cardiovascular disease or heart failure, plus type 2 diabetes (T2D) and/or hypertension, were enrolled. All were receiving stable maximum tolerated renin−angiotensin system inhibitors with or without SGLT2i. They were randomized 3:1 to runcaciguat once daily, titrated weekly (30–120 mg if tolerated), or placebo for 8 weeks. The primary efficacy endpoint was urine albumin-to-creatinine ratio (UACR) (average of post-randomization Days 22, 29, and 57 vs baseline). CONCORD was separately powered for CKD and T2D with stable SGLT2i comedication, CKD and T2D without SGLT2i, and non-diabetic CKD.

Results
Of 243 patients randomized, 229 were included in the full analysis set (FAS) and 170 in the per-protocol set (PPS). In the PPS, UACR decreased by −45.2% versus placebo with runcaciguat in patients with CKD without SGLT2i (P &lt; 0.001) and by −48.1% versus placebo in patients with CKD taking SGLT2i (P = 0.02) In the FAS, the relative reductions were −46.9% (P &lt; 0.001) and −44.8% (P = 0.01), respectively. No significant difference was observed between patients with or without SGLT2i. In non-diabetic CKD, UACR was reduced versus baseline with runcaciguat, but the change was not statistically significant (P = 0.10). Serious treatment-emergent adverse events were reported in 7% of patients receiving runcaciguat and 8% receiving placebo.

Conclusion
Runcaciguat improved albuminuria in patients with CKD, irrespective of concomitant SGLT2i. Runcaciguat was well tolerated. sGC activation may represent a novel kidney-protective treatment in CKD patients (funded by Bayer AG; ClinicalTrials.gov number, NCT04507061).