bluuebunny/crossref_metadata_2025_split huggingface dataset:
Data ownership in genomic research consortia
Authors: Nielsen Jane , Nicol Dianne 
Published: December 2024

ABSTRACT
Discourse around ownership of genomic sequence data has proliferated over recent years. There are likely to be few people who don’t feel a degree of connectedness to their genomic data. The inclusion of individuals’ genomic data in genomic datasets is critical to genomic research, and these datasets are most effective if shared widely. Genomic research consortia are an integral part of the genomic data sharing ecosystem, critical in facilitating data sharing among research groups. This article considers the property status of genomic data at various stages of the research life cycle, and the potential ‘ownership’ claims that may be made by various actors in data sharing networks. It does so by comparing the legal position with the findings of a study that examined policy documents and guidelines produced by international research consortia. This analysis enabled us to assess whether consideration of property interests is at the forefront of data sharing efforts, and if so, where such property interests are likely to reside.
Comorbidities in early-onset sporadic versus presenilin-1 mutation-associated Alzheimer disease dementia: Evidence for dependency on Alzheimer disease neuropathological changes
Authors: Sepulveda-Falla Diego , Villegas Lanau Carlos Andrés , White III Charles , Serrano Geidy E , Acosta-Uribe Juliana , Mejía-Cupajita Barbara , Villalba-Moreno Nelson David , Lu Pinzhang , Glatzel Markus , Kofler Julia K , Ghetti Bernardino , Frosch Matthew P , Restrepo Francisco Lopera , Kosik Kenneth S , Beach Thomas G 
Published: December 2024

Abstract
Studying comorbidities in early onset Alzheimer disease (AD) may provide an advantageous perspective on their pathogenesis because aging factors may be largely inoperative for these subjects. We compared AD comorbidities between early-onset sporadic cases and American and Colombian cases with PSEN1 mutations. AD neuropathological changes (ADNC) were very severe in all groups but more severe in the PSEN1 groups. Lewy body disease and cerebral white matter rarefaction were the most common (up to 60%) of AD comorbidities, followed by arteriolosclerosis (up to 37%), and large-vessel atherosclerosis (up to 20%). Differences between the 3 groups included earlier age of onset in the American PSEN1 cases, shorter disease duration in sporadic cases, and more frequent large-vessel atherosclerosis and cerebral amyloid angiopathy in the Colombian PSEN1 cases. Logistic regression models adjusted for age and sex found the presence of a PSEN1 mutation, an apolipoprotein ε4 allele and TDP-43 pathology to predict an earlier age of onset; Hispanic ethnicity and multiracial subjects were predictive of severe CAA. Comorbidities are common in early onset AD and should be considered when planning clinical trials with such subjects. However, they may be at least partially dependent on ADNC and thus potentially addressable by anti-amyloid or and/anti-tau therapies.
An analysis of RNA quality metrics in human brain tissue
Authors: Tian Jiahe , Lam Tiffany G , Ross Sophie K , Ciener Benjamin , Leskinen Sandra , Sivakumar Sharanya , Bennett David A , Menon Vilas , McKhann Guy M , Runnels Alexi , Teich Andrew F 
Published: December 2024

Abstract
Human brain tissue studies have used a range of metrics to assess RNA quality but there are few large-scale cross-comparisons of presequencing quality metrics with RNA-seq quality. We analyzed how postmortem interval (PMI) and RNA integrity number (RIN) before RNA-seq relate to RNA quality after sequencing (percent of counts in top 10 genes [PTT], 5′ bias, and 3′ bias), and with individual gene counts across the transcriptome. We analyzed 4 human cerebrocortical tissue sets (1 surgical, 3 autopsy), sequenced with varying protocols. Postmortem interval and RIN had a low inverse correlation (down to r = −0.258, P &lt; .001 across the autopsy cohorts); both PMI and RIN showed consistent and opposing correlations with PTT (up to r = 0.215, P &lt; .001 for PMI and down to r = −0.677, P &lt; .001 for RIN across the autopsy cohorts). Unlike PMI, RIN showed consistent correlations with measurements of 3′ and 5′ bias in autopsies (r = −0.366, P &lt; .001 with 3′ bias). RNA integrity number correlated with 3933 genes across the 4 datasets vs 138 genes for PMI. Neuronal and immune response genes correlated positively and negatively with RIN, respectively. Thus, different gene sets have divergent relationships with RIN. These analyses suggest that conventional metrics of RNA quality have varying values and that PMI has an overall modest effect on RNA quality.
Neurological Disorders and Use of Healthcare Services After Enteroviral Meningitis in Childhood: A Nationwide, Population-Based Cohort Study
Authors: Graham Emma E , Tetens Malte M , Bodilsen Jacob , Andersen Nanna S , Dessau Ram , Ellermann-Eriksen Svend , Franck Kristina , Midgley Sofie , Møller Jens Kjølseth , Nielsen Alex Christian , Nielsen Lene , Søgaard Kirstine K , Østergaard Christian , Lebech Anne-Mette , Nygaard Ulrikka , Omland Lars H , Obel Niels 
Published: December 2024

Abstract

Background
Nervous system infections are associated with long-term risks of neurological disorders and healthcare service utilization, but little data exist on the long-term risks of enteroviral meningitis in childhood.

Methods
We performed a population-based, nationwide registry-based matched cohort study (1997-2021). We included 925 children with enteroviral meningitis aged &lt;17 years, a comparison cohort, and a cohort of siblings of all individuals. To illustrate short- and long-term risks of neurological disorders, we calculated 1-year cumulative incidences and age- and sex-adjusted hazard ratios (aHRs) with 95% confidence intervals (95% CIs) during years 1-20 of follow-up. We further calculated the annual proportion of individuals using antiepileptic medication and healthcare services.

Results
Young infants (0 to &lt;90 days) and older children (≥90 days to &lt;17 years) had slightly increased short- and long-term risks of neurological disorders after enteroviral meningitis compared to comparison cohort members (1-year cumulative incidence: 1.4% vs 0.6%, and 1.5% vs 0.4%, 1-20-year adjusted hazard ratio: 2.0 [95% CI: 1.2-3.2] and 1.7 [95% CI: 1.0-2.8]). Older children had increased use of antiepileptic medication, as well as the use of health care services both before and after enteroviral meningitis, with a similar trend among their siblings.

Conclusions
Enteroviral meningitis in childhood appears to be associated with increased risk of short- and long-term neurological morbidity, though our estimates in older children may be confounded by prior neurological morbidity or increased healthcare-seeking behavior. Our findings suggest a generally good prognosis after enteroviral meningitis, though clinicians should be aware of the risk of neurological disorders in selected patients.
(014) THE EVOLUTION OF PATIENT SATISFACTION AND WELL- BEING OVER TIME FOLLOWING INFLATABLE PENILE PROSTHESIS
Authors: Pinkhasov A , Guillen A , Bonakdarhashemi M , Helo S , Ziegelmann M , Kohler T 
Published: December 2024

Abstract

Introduction
Penile prosthesis (PP) implantation is associated with high patient satisfaction in patients with medically refractory erectile dysfunction (ED). There remains a paucity in the literature regarding the temporal evolution of patient satisfaction and well-being following PP surgery.

Objective
We aimed to identify factors responsible for patient satisfaction after surgery.

Methods
We initiated a registry of patients undergoing surgery for placement of a PP. After consent, perioperative study assessments and follow-ups were conducted. After surgery, patients were directed to a survey at 6 months and 12 months. Patients who completed both items were included in the analysis.

Results
A total of 304 patients had a PP placement, of these 101 completed the initial surveys. Overall patient satisfaction was favorable and durable and 6- and 12-months (87% and 82% respectively, p = 0.11). Confidence with device use was reported by 92% at 6 months, without significant change at 1 year (vs. 95%, p = 0.91). At 6 months, 81% of patients reported that their PP met or exceeded expectations, 83% of patients reported that they would undergo the procedure again, and 80% would recommend to a friend/family member. [Figure 1] At 6 months, 78 patients (77%) reported a moderate to high improvement in their overall sense of well-being related to their PP. This percentage further increased to 91% at 12-months (p &lt; 0.001). Additionally, 36% of patients reported that they had made significant improvements to their overall lifestyle since receiving the PP, and this increased to 48% by 12 months post-operatively (p = 0.082).

Conclusions
Penile prosthesis satisfaction is evident and durable as early as 6 months following surgery. Factors such as perceived overall well-being continued to significantly improve past 6 months, and nearly half of patients reported overall lifestyle improvement following surgery.

Disclosure
Yes, this is sponsored by industry/sponsor: Coloplast.
Clarification: Industry funding only - investigator initiated and executed study.
(058) DOES TREATING OBSTRUCTIVE SLEEP APNEA HELP WITH STUTTERING PRIAPISM? A CASE STUDY
Authors: Tabei SS , Alvey L , Baas W 
Published: December 2024

Abstract

Introduction
Patients with sickle cell anemia are prone to developing stuttering priapism. Contributing factors include red blood cell deformation, vascular occlusion, nitric oxide dysregulation, endothelial dysfunction, and hypoxia. Some studies have indicated that oxyhemoglobin desaturation occurs at a higher rate during sleep and may lead to priapism episodes in patients with an underlying risk factor.

Objective
To assess the role of continuous positive airway pressure (CPAP) and improvement in obstructive sleep apnea symptoms in reducing night-time priapism episodes in a patient with sickle cell anemia.

Methods
A 43-year-old man who was a known case of sickle cell anemia presented to us with a 3-year history of recurrent episodes of stuttering priapism. Interestingly, these episodes occurred exclusively at night during his sleep which caused major disruption to the normal sleep pattern. The patient was initially commenced on hydroxyurea and pseudoephedrine which did not result in definitive improvement. Additional therapy such as adding terbutaline or increasing the dosage of hydroxyurea dosage by his hematology team was also inconclusive in reducing the burden of priapism. Other treatment options such as daily tadalafil was also trialed in this patient but did not show any improvement. At this stage, we decided to start the patient on bicalutamide which resulted in partial resolution of symptoms. A thorough review of the patient’s history revealed that he was a loud snorer and had not sought any treatment for this condition. We referred the patient for sleep evaluation and determined that he was suffering from concurrent obstructive sleep apnea. The patient was started on CPAP therapy and short-term follow-up at 3 months showed a resolution of priapism episodes following the addition of this treatment modality.

Results
Despite positive findings in our case, it cannot be fully determined whether or not the CPAP therapy was a definitive solution to relieving the priapism episodes. This improvement however warrants a closer look at the concurrent occurrence of obstructive sleep apnea and stuttering priapism in the setting of sickle cell anemia. Healthcare providers may inform sickle cell anemia patients regarding established obstructive sleep apnea screening protocols such as the STOP-BANG questionnaire.

Conclusions
The role of obstructive sleep apnea in the setting of sickle cell anemia-induced priapism is rather understudied. Further long-term trials are required to determine the definitive role of CPAP therapy in the setting of sickle cell anemia-induced stuttering priapism and obstructive sleep apnea.

Disclosure
No.
(062) THE RISK OF BIOCHEMICAL RECURRENCE OF PROSTATE CANCER IN MEN RECEIVING TESTOSTERONE REPLACEMENT THERAPY FOLLOWING RADICAL PROSTATECTOMY
Authors: Rust JO , Pereira TA , Smith R , Boris R , Egemba C , Green J , Koch M , Laniak L , Bahler C , Beneth Iv R , Spio M , Bernie HL 
Published: December 2024

Abstract

Introduction
Modern evidence and new theoretical frameworks have significantly challenged long-held beliefs about androgens and Prostate Cancer (PCa). However, there remain substantial controversies, especially concerning the use of testosterone therapy (TTh) in men with any history of PCa.

Objective
Analyze the risk of biochemical recurrence (BCR) of PCa in men who received TTh compared to men who did not receive TTh following radical RP.

Methods
Patients who underwent an RP from 2013-2023 with total testosterone (TT) and PSA levels were included. The risk groups were defined as the following: PSA &lt;10 and grade group 1 (Gleason 6) as Low Risk; PSA is between 10 and 20, or grade group 2 or 3 (Gleason 7) as Intermediate Risk; PSA &gt;20, or grade group 4 or 5 (Gleason 8 to 10), including T3b or T4 pathology as High Risk. BCR is defined as PSA &gt; 0.2. Low testosterone (T) was described as a total T (TT) level &lt; 300 ng/dL on two occasions using LCMS collected before noon. Men were grouped based on risk groups, and T levels and TTh use were recorded. Men were divided into TT &gt;300 and no TTh (NT); TT &lt;300, who did not receive TTh (LT-); TT &lt;300, who received TTh (LT+); TT &gt;300, who received TTh (NT+). Rates and time to BCR were recorded. Chi-square analysis and Fisher’s Exact test were performed for group comparisons. Kruskal Wallis Test was used to compare medians with log-rank (mantel-cox) significance reported. Kaplan Meier survival analysis was performed for time to BCR and time to follow-up. For all statistical analyses, clinical significance was assessed at p &lt; 0.05. Individuals with missing values were not included in the analyses. All statistical analysis was conducted using SPSS.

Results
1105 men, with a median age of 63, were included. 1.6% had low risk (LR), 41.6% intermediate risk (IR), and 56.8% had high risk (HR) PCa. The median follow-up time was 50 months, and the median to BCR was ten months. 42% of patients were NT, 50.7% LT-, 3.4% LT+, and 3.9% were NT+. There was a significant difference in BCR rates between NT, LT-, LT+, and NT+ within the intermediate and high-risk groups (p &lt; 0.001), with the HR PCa group having the highest BCR rate (46.9%). Within the HR PCa men, the LT- group had the highest BCR rate (61.5%) compared to the HR NT+, which had the lowest BCR at 20%. Lastly, LT- group had the lowest median time to recurrence (4 months) compared to LT+ which had the longest (51 months). (p = 0.020). (Figure 1).

Conclusions
TTh in men with PC does not increase rates of or time to BCR.

Disclosure
Any of the authors act as a consultant, employee or shareholder of an industry for: Coloplast; Boston Scientific; BK Ultrasound.
(071) NON-PROPRIETARY SUBCUTANEOUS TESTOSTERONE REPLACEMENT THERAPY FOR HYPOGONADAL MEN
Authors: Mossack S , Spellman A , Desouky E , Nabulsi O , Loos D , Levine L 
Published: December 2024

Abstract

Introduction
Advancement in the treatment for male hypogonadism involves investigation into safer, less expensive, and more effective alternatives than currently available treatment modalities, with subcutaneous testosterone replacement therapy (SubQ TRT) offering an attractive solution to several patient concerns.

Objective
To assess the use of non-proprietary SubQ TRT as treatment for hypogonadal men and its effect on HCT, PSA, and patient satisfaction.

Methods
This is a retrospective chart review of 93 men, mean age 60.6 years, receiving SubQ TRT with a mean follow up length of 17.9 months (range 0-52 months). Patient data was collected prior to initiation of therapy and at subsequent visits. Serum testosterone, HCT, and PSA were determined through regular blood draws, and patient demographics, AUA Symptom Index (AUA SI), Sexual Health Inventory for Men (SHIM) Scores, and patient satisfaction were collected at patient visits or via patient communication through email and phone. Univariate analysis and paired t-tests were used to analyze study variables.

Results
93 patients received SubQ TRT. Mean changes in total testosterone level (increased 125.77 ng/dL, p-value&lt;0.001), hematocrit (increased 1.2%), PSA (increased 0.3 ng/dl), SHIM score (increased 0.9 points) and AUA symptom score (decreased 0.3 points) were calculated at the patients’ initial and follow up visits while on SubQ TRT. Sixty-eight (73%) patients had been on various combinations of TRT before switching to SubQ: IM, CC, Testopel, T-Gel, HCG, and Anastrozole. Patient satisfaction surveys were completed by 57 patients (61%), with 26 (78.9%) patients reporting satisfaction with SubQ TRT versus 28.1% with past forms of TRT. Patients reported SubQ TRT to be both easier (71.4%) and generally preferred (71.1%) over their previous form of TRT. Several patients stopped SubQ TRT including one patient with stroke. Lastly, a cost analysis using the average available GoodRx prices in the Chicagoland area showed that a 1-month supply of non-proprietary testosterone cypionate was $235.45 less than Xyosted (the only FDA-approved SubQ TRT for management of male hypogonadism).

Conclusions
Use of non-proprietary testosterone cypionate as TRT results in an elevation in serum testosterone with favorable side effect profiles and overall patient satisfaction.

Disclosure
Any of the authors act as a consultant, employee or shareholder of an industry for: Consultant to Absorption Pharmaceuticals, Boston Scientific, Hybrid Medical, International Medical Devices and Irrimax Corp.
(076) THE MOBYUS CONSORTIUM: DEMOCRATIC, DECENTRALIZED, DYNAMIC MALE INFERTILITY RESEARCH
Authors: Naelitz B , Bushweller L , Nam C , Nicholson T , Deibert C , Andino J , Raheem O , Shin D , Doolittle J , Mehta A , Hehemann M , Campbell K , Eleswarapu S , Lundy S 
Published: December 2024

Abstract

Introduction
Despite a prevalence of nearly 1 in 10 men, male infertility remains incompletely understood and half of all diagnoses remain idiopathic despite extensive diagnostic workup. Even at large institutions, the rarity of many subpopulations of infertile men limits sample size and data quality.

Objective
We initiated an integrated multi-institutional research consortium to better under the pathogenesis of male infertility and improve our ability to conduct diverse, clinically relevant evidence-based research in this area.

Methods
A standardized 400-point database with advanced branching logic and automated calculation capabilities was generated and iteratively optimized using the HIPAA-compliant REDCap platform. Individual instruments were produced to capture demographic information, medical history, physical examination findings, lab and semen testing results, procedural and surgical data, and fertility outcomes. The database can be rapidly deployed at new institutions following completion of a standard data use agreement and is internally maintained by site investigators and exported at regular intervals for consortium-wide aggregation in a de-identified fashion.

Results
With the primary goal of pursuing collaborative and democratic research, the IRB-approved MOBYUS (Male Organ Biology Yielding United Science) consortium currently consists of at least twelve large US-based academic medical institutions. Data collection is ongoing with &gt;4000 patients included to date with new projects are identified at regular monthly virtual meetings. The group has successfully published three proof-of-principle manuscripts to date.

Conclusions
As the field of urology and its subspecialties move towards collaboration and data-driven management, male infertility and its associated rare diseases may benefit from a decentralized network capable of leveraging large data sets. The MOBYUS Consortium aims to accomplish this goal for male infertility patients with an emphasis on generating the best possible clinical data for the patients suffering from this difficult condition. The collaborative approach adopted by the MOBYUS Consortium has the capability of rapidly generating a robust cohort for practice-shaping studies.

Disclosure
Any of the authors act as a consultant, employee or shareholder of an industry for: Fellow Health (Dr. David Shin, Stockholder); Posterity Health (Dr. Akanksha Mehta, Advisory Board Member); Boston Scientific Corporation (Dr. Marah Hehemann, Consultant); Coloplast Corporation (Dr. Marah Hehemann, Consultant); Endo International (Dr. Marah Hehemann, Speaker).
(079) RELIGION’S IMPACT ON DECISION MAKING AND COPING FOR MALE-FACTOR INFERTILITY COUPLES
Authors: Garcia Keeme-sayre A , Kassab J , Oppenheimer A , Duan M , Huang J , Stocks B , Lipshultz L 
Published: December 2024

Abstract

Introduction
With ideas such as God’s command to “be fruitful and multiply” in both Jewish and Christian texts and the Vatican’s disapproval of the use of in vitro fertilization (IVF), religious identities of male-factor infertility patients may affect how patients engage in reproductive health care.

Objective
The goal of this study is to assess the saliency of religious beliefs on the male-factor infertility patient.

Methods
A REDcap survey was sent to patients who presented for an infertility visit between 10/2/2022-10/2/2023. Using a 4-point Likert Scale and written responses, participants reflected on their religion’s role in their selection of treatment. Written responses were analyzed for common themes and results were reported using descriptive statistics.

Results
73% of respondents (n = 285/392) identified with a religion (90% a form of Christian, 3.2% Non-Orthodox Jewish, 3.2% Muslim, and 3.6% Other Religions). Non-Denominational (ND) or Protestant (P) Christians, Catholics, and Muslims reported that their religion encouraged the use of expanded infertility treatment rather than caused hesitancy (Table 1). Among written responses, IVF or Intrauterine Insemination was the most suggested infertility treatment (47.5% (n = 19/40)), and donor sperm or egg was the most discouraged (52% (n = 12/23)). Muslims were most likely to report discouragement of donor sperm or egg (n = 6/9 (66.7% of Muslims)). 243 participants provided written insight into their religious views of infertility treatment. Aside from no religious impact (45.7%), the most common themes were: no personal conflict with religious views (20.7%), reproduction as a core religious tenet (10.7%), and the unity of religion and science (9.9%). A small number of participants (7.9%) discussed having disagreed with or gone against their religion’s views, the majority of which were Catholic (n = 13/17 (76.5%)).

Conclusions
Religion was an encouraging factor for most male patients seeking infertility treatment. However, physicians should still take care to acknowledge differences among religions, recognizing that certain treatment options may cause discomfort in religious patients.

Disclosure
No.