bluuebunny/crossref_metadata_2025 huggingface dataset:
(256) INFLUENCE OF SOCIOPOLITICAL AND ECONOMIC ISSUES ON VASECTOMY DECISIONS: A QUALITATIVE STUDY AMONG PATIENTS
Authors: Cheng L , Natesan D , White K , Jarlenski M , Chang J , Hwang K
Published: December 2024

Introduction

In recent years, vasectomy rates have strongly positively correlated with the emergence of societal and economic issues, such as The Great Recession and rising unemployment rates. Since 2020, there have been numerous events of sociopolitical and economic importance in the U.S., including the emergence of COVID-19 as a global pandemic; subsequent domestic consumer price inflation; and the reversal of federal protections for the right to abortion under Roe v Wade. Following the June 2022 reversal, vasectomy interest rose significantly despite no direct impact to male contraception. This increase suggests an understudied influence of societal issues on individuals’ reproductive healthcare decisions.

Objective

Our objective was to explore patient perspectives of how recent sociopolitical and economic issues (ie, Dobbs v Jackson ruling, post-COVID consumer price inflation) influenced their vasectomy decision and timing.

Methods

We interviewed 20 men aged 18 years or older who had initiated a vasectomy consult or appointment after June 2022. Participants were purposively selected based on their age (those 30 years or younger); men with no biological children at time of vasectomy; and men who indicated on an intake survey that sociopolitical or economic issues factored into their vasectomy decision. A qualitative descriptive thematic analysis approach was used to develop a codebook that included deductive and inductive coding. The constant comparative method was used to review coding and identify similar and differing themes across participant experiences.

Results

Many participants expressed that outside of personal reasons for pursuing vasectomy, sociopolitical and economic issues were significant motivators for their vasectomy decision and timing. Several described how increased discourse and uncertainty around all forms of contraception access following Dobbs fostered their desire to be “proactive” through vasectomy. Others lamented the unprecedented difficulty providing for a child given significant economic inflation of food costs and other necessities.

Conclusions

Recent sociopolitical and economic issues significantly influenced male patients’ decisions to undergo a vasectomy despite no direct impact to male contraception options. Future research directions include intersectional exploration with patients from diverse racial, cultural, and geographic backgrounds.

Disclosure

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(261) DIGITAL PROMOTION OF INFERTILITY COVERAGE FOR TRAINEES IN UROLOGY RESIDENCY PROGRAMS
Authors: Kassab J , Garcia Keeme-sayre A , Oppenheimer A , Rasun S , La T , Andino J , Lipshultz L
Published: December 2024

Introduction

Physicians face significantly higher rates of infertility than the general public and over 50% of medical residents express concerns over their own fertility. This highlights a pressing issue within the medical community, particularly among those in surgical training programs. Addressing these concerns is crucial for the well-being and future planning of medical professionals, especially as certain institutions have begun to offer coverage for fertility services in employer-sponsored insurance plans.

Objective

To evaluate the accessibility of online information describing infertility coverage for resident physicians by accredited United States urology residency programs.

Methods

Utilizing the AUA’s listing of accredited U.S. Urology Programs, we investigated each program website to assess for mention of fertility benefits and coverage offered for trainees. Regardless of the information found at the primary program websites, we conducted a second inquiry via a thorough internet search to find any mention of fertility coverage offered at individual institutions. Fertility benefits were defined as coverage for any of the following: fertility evaluation, intrauterine insemination (IUI), in-vitro fertilization (IVF), surgical treatment, egg/sperm storage, fertility medications, and/or adoption services. The programs were then sorted into four groups depending on available online information: 1.) No mention of fertility benefits; 2.) Information regarding coverage was alluded to but behind a required institutional login or portal; 3.) Fertility benefits/coverage was mentioned on the website and is offered to its trainees; 4.) Fertility benefits/coverage was mentioned on the website but is not offered to its trainees. Descriptive statistics were performed on the dataset using SPSS.

Results

Of the 156 urology program websites, nearly 75% did not mention fertility coverage options at all (Figure One). On their main residency website, 15.4% mentioned that they provide fertility coverage for their residents, 2.6% explicitly mentioned that they do not provide fertility care through their insurance plans, and in 8.3%, fertility coverage information was not accessible due to institutional login/portal. Lastly, through the broader search, 42.3% of institutions with an associated urology program did not mention fertility benefits. In 48.7% of health systems, fertility benefits were mentioned and offered.

Conclusions

Despite growing concerns in the medical community about the fertility impact of demanding residency programs and delaying childbearing, there is a lack of transparency regarding fertility coverage on urology residency websites. Clear and accessible information regarding infertility coverage would enable trainees to make more informed decisions when selecting the rank of residency programs, ensuring that they can adequately plan for their personal and professional futures.

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(282) A PROPOSED SURGICAL TECHNIQUE TO CREATE A NATURAL-APPEARING RECESSED VAGINAL INTROITUS WITH GENDER-AFFIRMING “SHALLOW-DEPTH VAGINOPLASTY” (VULVOPLASTY) UTILIZING A PEDICLED ADVANCEMENT FLAP
Authors: Shiang A , Dadashian E , Sandhu S , Mallavarapu S , Smith S , Garcia M
Published: December 2024

Introduction

Feminizing genital gender-affirming surgery (fgGAS) options include vaginoplasty with- (“full-depth vaginoplasty”), or without neovaginal canal (“vulvoplasty” or “shallow-depth vaginoplasty (SDV)”). If a transgender woman does not desire receptive vaginal intercourse, SDV is an excellent option, eliminating lifelong dilation/douching and lower complication risks. Achieving “normal appearing” feminine anatomy is critical for these patients. Currently, techniques for SDV rely on a full thickness skin graft.

Objective

1) To better understand decision-making factors when undergoing SDV. 2) To describe a novel technique used to create a recessed vaginal introitus. 3) To evaluate patient perceptions of appearance as compared to cisgender vulvae.

Methods

Patients undergoing fgGAS between 04/2017-07/2022 were included. Of the patients undergoing SDV, an anonymous electronic survey querying decision-making factors and overall post-operative satisfaction was undertaken. In addition, our novel technique is described.

Results

110 patients underwent fgGAS. Of these, 35/110 (32%) underwent SDV. Priorities: Achieving an appearance “comparable to” cisgender vulvae was ranked second highest after “elimination of male genital anatomy” (Fig. 1a). Technique: To achieve a recessed skin-lined vaginal introitus, gathering sutures create a “dimple” from penile/scrotal skin flap based off the posterior perineum, tethered to the tendon of the bulbospongiosus muscle, behind the urethral bulb (Fig. 1b-e). Attractiveness (Fig. 1f): When compared to cisgender vulvae of similar age/weight, 26/26 (100%) patients reported their vulvae had “similar” or “somewhat similar” appearance to cisgender vulvae. 24/26 (92%) of patients found their vulvae to be either “similarly or more attractive”, and 2/26 (8%) found their vulvae to be “less attractive” as compared to cisgender vulvae.

Conclusions

Women opting for SDV greatly consider cosmetic appearance which must be indistinguishable from cisgender female anatomy. This appears to be offered by this technique. In addition, this technique offers women the opportunity to have external anatomy in line with their gender identity, and for women not interested in using a vaginal canal for receptive vaginal intercourse, this option foregoes the added risks and commitment to lifelong dilation and douching.

Disclosure

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(297) PENILE CALCIPHYLAXIS PRESENTING WITH TERTIARY HYPERPARATHYROIDISM: A CHALLENGING CASE REPORT
Authors: Sávio LF , Cardoso JF , Campos L , Taromaru E
Published: December 2024

Introduction

Penile calciphylaxis (PC) is an uncommon and potentially life-threatening syndrome with an estimated 6-month mortality rate. PC is characterized by the obstruction of small vessels within the subcutaneous adipose tissue and dermis of the penis. The precise etiology of calciphylaxis is not entirely understood, but it is frequently associated with conditions such as end-stage kidney disease (ESKD), chronic kidney disease (CKD), and the use of medications like warfarin. Symptoms of PC may include pain, discoloration, and the formation of non-healing ulcers on the penis. Management of PC involves controlling medical risk factors to mitigate vascular calcification, alongside interventions such as surgical debridement, penectomy, and local wound care.

Objective

We report a case of a patient with ESKD who presented with necrotic ulcers of his penis and was found to have tertiary hyperparathyroidism.

Methods

A 69-year-old male patient was referred to our institution due to a distressing necrotic lesion encompassing 60% of the glans penis over the preceding two months. His medical history includes tertiary hyperparathyroidism, diabetes, hypertension, cardiomyopathy, and ESRD (grade V). The patient underwent renal transplantation; however, two years after the transplant, he lost kidney function and returned to dialysis. Laboratory analyses revealed significantly elevated levels of parathyroid hormone (PTH) at 1350 pg/ml, calcium at 1.34 mmol/L, and vitamin D at 30 ng/ml. A pelvic CT scan revealed a pervasive pattern of calcification within the aorta, branches of the celiac axis, and penile vessels (Fig. 1 and 2). Patient was initially started on broad-spectrum antibiotics, including ciprofloxacin, azithromycin, and ceftazidime with any improvement. Cultures from the blood and gangrenous site were negative.

Results

Treatment with sodium thiosulfate was initiated in conjunction with daily PDE-5-inhibitors for 2 – months before complete parathyroidectomy. Pain score from the penile ulcers started to regress along with the complete reepithelization of the ulcer. At 2 – years of follow up from the initial treatment patient is still alive with any other new onset of the ulcers.

Conclusions

PC represents a significant life-threatening condition in patients with ESRD with a compromised overall survival as reported in the literature. The uniqueness of our study lies in the combined use of a PDE-5 inhibitor along with parathyroidectomy to overcome the nature of the disease, leading to improved patient quality of life. Nonetheless, due to severity of the disease there’s need for.

Disclosure

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(312) WHAT DO WE KNOW ABOUT ADULT BABY DIAPER LOVER (ABDL) SEXUALITY? A SCOPING REVIEW
Authors: Haymovitz E , Rosenman J , Karpman H , Haggarty A
Published: December 2024

Introduction

Adult Baby Diaper Lovers (ABDL) is a lifestyle, an identity, and community by and for consenting adults who share a common fetish in diapers. Paraphilic infantilism, or 'Adult Baby Syndrome', is the historic term used to describe this fetish, and it refers to a mental illness (Stekel, 1930; Pate & Gabbard). These terms are no longer politically correct, as the ABDL experience is no longer classified by the DSM 5 or ICD as a paraphilia (Murphy, Bradford, and Fedoroff, 2020).

Objective

The purpose of this study was to explore what is known about ABDL health and mental health by conducting a scoping review of the literature in the social and medical sciences.

Methods

The four presenters employed Covidence software and expansive search terms to screen and extract data from research articles identified in SCOPUS, MEDLINE, and Psychino. Search terms were: TITLE-ABS-KEY ((fetishism OR infantilism OR {Adult Baby?Diaper Lovers} OR abdl OR ab?dl OR (paraphili* W/2 infantilism) OR {Adult Baby Syndrome} OR "Diaper fetish*" OR diaperism OR (diaper AND (sex* OR kink)) OR autonepiophilia OR ageplay) AND (adult)).

Results

Discrepancies were resolved by consensus. After duplicates were removed in Covidence software, the protocol yielded 909 articles, 647 in Scopus, 359 in MEDLINE, and 92 in PsycINFO, and after thorough screening, these resulted in 42 studies for systematic review. Among books articles reviewed were theoretical explorations of psychological infantilism in Russia, a book on the psychoanalytic underpinnings of psychosexual infantilism from Germany, and several contemporary works addressing ABDL directly.

Conclusions

The majority of the literature on diaper fetishism and ABDL is historically associated with the period of time during which there was a diagnostic category available for paraphilic infantilism, and more recently, an identity category for ABDL. However, there remains a noticeable gap in the literature on the subject., Several foreign language articles and books, including those from Russia, Poland, and Germany, when taken together, do seem to comprehensively address the subject of psychosexual infantilism and diaper fetishism, the majority of North American literature appears to be associated with psychoanalytic case studies or the sensationalized subject heading of "adult baby syndrome". We conclude that this construct is woefully misunderstood, stigmatized, and hidden, because of poor coverage in the scientific literature.

Disclosure

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(313) PENILE PROSTHETIC PIONEER: F. BRANTLEY SCOTT
Authors: Ffurtado T , Lavold A , Loeb C , Bash J , Andino J , Jayadevan R , Mills J
Published: December 2024

Introduction

Dr. F. Brantley Scott (1930-1991) was a pioneer of prosthetic urology in the early 1970s, revolutionizing the treatment of erectile dysfunction (ED) and urinary incontinence. This abstract explores the life and groundbreaking contributions of Dr. Scott, emphasizing his development of the artificial urinary sphincter (AUS) and inflatable penile prosthesis (IPP).

Objective

To provide a comprehensive review of the history of Dr. F. Brantley Scott.

Methods

Extensive web-based research and historical accounts by those who knew him provided the primary source of information.

Results

Born in Pearsall, Texas in 1930, Dr. Scott embodied the larger-than-life Texan spirit with charm and brilliance, and he was often seen in his signature cowboy boots, massive belt buckle, and cowboy hat. His journey took him from an undergraduate at the University of Texas at Austin to Baylor College of Medicine where he completed his urology residency, ultimately rising to become a full professor at Baylor and chief of urology at the VA Hospital and St. Luke’s Episcopal Hospital in Houston. Dr. Scott’s devotion to teaching and mentorship fostered the development of eponymous implant luminaries Drs. William Furlow, John Mulcahy, and Steven Wilson. He popularized urodynamics for bladder function assessment and played a pivotal role in the development of the AUS. While tinkering with AUS hydraulics, he used a silicone elastomer from the US space program to develop the first IPP, initially known as the Scott prosthesis. Despite the prevailing belief in the psychological origins of impotence, he challenged the status quo and brought prosthetic urology into the limelight. While not the first to patent the IPP (credited to Dr. Barish Strauch), Dr. Scott’s collaboration with American Medical Systems (AMS) made the IPP a reality for patients. Dr. Scott’s patient selection process for IPP included comprehensive psychiatric evaluations and nocturnal penile tumescence measurements in sleep labs, revealing the connection between REM sleep and nocturnal erections. A true renaissance man, he was a pilot, author, artist, sculptor, rancher, musician, engineer, and entrepreneur. He retired in 1990 to pursue his passion for flying, but tragically lost his life during a test flight of a self-constructed plane near his Texas home in 1991.

Conclusions

Dr. F. Brantley Scott was a true visionary and pioneer of prosthetic urology. His groundbreaking work developing the AUS and IPP, combined with his larger-than-life Texan spirit, continue to influence urology, honoring his legacy as an innovative brilliant figure in the field.

Disclosure

Any of the authors act as a consultant, employee or shareholder of an industry for: Boston Scientific, Endo Pharmaceuticals and Halozyme Therapeutics.
(325) SINGLE-PORT ROBOTIC APPROACH TO RETRIEVAL OF MIGRATED INTRAVESICAL INFLATABLE PENILE PROSTHESIS RESERVOIR
Authors: Fakes C , Huang J , Stocks B , Johny A , Lipshultz L , Link R
Published: December 2024

Introduction

Migration of an IPP reservoir into the bladder is a rare, but known complication of penile prosthesis surgery with few documented cases over the past 25 years. Management options include retrograde removal via a penoscrotal/infrapubic approach without cystotomy closure and prolonged foley placement, versus an antegrade, open approach via an open cystotomy, closure of the bladder defect, and a similarly prolonged foley placement. The patient is a 67-year-old male with a non-functional IPP. He underwent a complete IPP explanation and replacement with a new device via a penoscrotal approach. The surgery was uncomplicated, and the patient was discharged home on post-operative day 1. The patient presented to the Emergency Department 4 days later with erythema spreading from the surgical site, concerning for cellulitis and possible infection. A CT scan demonstrated significant soft tissue changes as well as migration of the IPP reservoir into the urinary bladder. The decision was made to proceed with complete explantation of the penile prosthesis. Due to the complexity of the patient’s surgical history, body habitus, and the reservoir location, we proceeded with robotic-assisted laparoscopy via a transvesical approach using the Da Vinci SP platform.

Objective

We present a novel approach for removal of an intravesical IPP reservoir and cystotomy closure using the Da Vinci SP platform.

Methods

This video details the surgical approach to IPP explantation and removal of migrated intravesical IPP reservoir. The Single-Port Da Vinci robotic system was used for an intravesical approach to removal of the migrated reservoir and closure of the iatrogenic cystotomy.

Results

Post-operatively, the patient’s hospital course was complicated by an ileus which resolved with 3 days of nasogastric tube and bowel rest, as well as a popliteal DVT for which he was started on Eliquis. He was discharged on post-operative day 7 and foley catheter was removed post-operative day 10.

Conclusions

There were several benefits to using the single-port robotic approach. We had better visualization of the iatrogenic cystotomy than would have been possible via an open or laparoscopic approach. The single-port robot also required a much smaller incision than an open approach, allowing decreased morbidity of the procedure. Finally, there was the benefit of shorter foley catheter duration, as it was removed after 10 days. In conclusion, the single-port robotic approach was a successful and less morbid approach to retrieval of a migrated intravesical IPP reservoir.

Disclosure

No.
(328) RELATION BETWEEN TIME OF PRESENTATION OF ERECTILE DYSFUNCTION (ED) AND SEARCH FOR INFORMATION ON THE INTERNET WITH IIEF-5 SEVERITY SCORE
Authors: Reyes-Vallejo LA , Gonzalez-Carranza HR
Published: December 2024

Introduction

Erectile Dysfunction is a common disease of the male reproductive system, which seriously affects the life quality of patients and their partners.

Objective

Our purpose is to assess the time between the onset of symptoms and the seeking of medical attention for Erectile Dysfunction (ED). We hypothesize that patients with ED searching for information in unreliable sources increases time between symptoms onset and the first medical consultation.

Methods

A questionnaire was given to patients diagnosed with ED during urological consultation (June 2023–June 2024). Questionnaire included questions about seeking information on the Internet, their findings, their source of information, their search motive, the date of onset of ED symptoms and the first time they went to a medical consultation for this reason. IIEF-5 questionnaire was applied to measure the severity of the ED, dividing it into 4 groups (mild, mild–moderate, moderate and severe).

Results

154 questionnaires were collected. Of the patients, 3 (1.95%) had no ED, 40 (25.97%) had mild ED, 61 (39.61%) had mild–moderate ED, 39 (25.32%) had moderate ED and 11 (7.14%) had severe ED. Average age was 51 years (22-82). Average time between the onset of symptoms and the first consultation was 23.7 months (0-178). 94 (61%) of the patients had previously searched for information on the Internet. There was a significant relationship with severity and internet search (p < 0.001). We found a significant relationship between greater severity of ED and less time seeking medical treatment for the mild, mild–moderate and moderate groups (p < 0.001, p < 0.001, p < 0.001). Severe ED group did not have a significant value (p = 0.03). Patients who had previously searched for information on the Internet had a larger time to attend first consultation (p < 0.001).

Conclusions

Patients take an average of 23.7 months from the onset of symptoms of erectile dysfunction until attending consultation Patients with greater severity come for consultation later, except for patients with Severe ED Patients who searched for information on the Internet take longer to attend consultation.

Disclosure

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Assessing the efficacy of postbiotics derived from Lactobacillus plantarum on antibiotic resistance genes in nosocomial pathogens such as Enterococcus faecalis and Pseudomonas aeruginosa
Authors: Nezhadi Javad , Ahmadi Ali
Published: December 2024

This study investigated the antibacterial and anti-biofilm properties of postbiotics derived from Lactobacillus plantarum and their effect on the expression of antibiotic resistance genes (ermB and blaKPC) in Enterococcus faecalis and Pseudomonas aeruginosa, respectively. Cell-free supernatants (CFSs) were analyzed through gas chromatography–mass spectrometry (GC-MS), which showed that butyric acid (14.31%) was the major compound, other metabolites present in CFSs included lactic acid (5.94%), hdroxyacetone (5,21%), benzoic acid (3.12%), Pyrrolo[1,2-a] pyrazine-1,4-dione (1.91%), 2,3-Butanediol (1.04%), and 2,3-dihydro-3,5-dihydroxy-6-methyl-4H-pyran-4-one (0.73.%). To investigate the effect of postbiotics on bacterial growth and biofilm formation, minimal inhibitory concentration (MIC) and microtiter plate assays were used. MIC results showed that resistant En. faecalis and P. aeruginosa can grow at concentrations of 2.5 and 5 mg/ml, respectively, after exposure to postbiotics. Furthermore, the microtiter plate results showed that postbiotics significantly reduced biofilm formation: 51%, 45%, and 39% in En. faecalis and 46%, 38%, and 27% in P. aeruginosa at different concentrations. Real-time polymerase chain reaction also confirmed the reduction of resistance genes (ermB; P = 0.007 and blaKPC; P = 0.02) expression. MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) assay showed that the cell survival rate was 80%. These findings suggest that postbiotics from L. plantarum may be a promising approach for combating bacterial growth, biofilm formation, and antibiotic resistance.
Salman Rushdie and postsecularism: The Satanic Verses and the postcolonial Bildungsroman
Authors: Jussawalla Feroza
Published: December 2024

This article reads Salman Rushdie’s The Satanic Verses as a Bildungsroman that is postcolonial and postsecular. Among the distinctiveness of the postcolonial Bildungsroman is that it can present a protagonist who can negotiate among nationality, religion, secularism, and postsecularism. This article contextualizes The Satanic Verses within Islamic poetic forms and Rushdie’s secular upbringing in postcolonial India. This context shows how Rushdie, rather than blaspheming the Prophet Muhammad, approaches the Prophet’s life story with postsecular wonder and awe. This postsecularism is not a turn towards religion but a means of approaching cultural myths.
Unsayable word: gurbāni, Punjabi poetry, and the postsecular impulse
Authors: Mandair Arvind-Pal S
Published: December 2024

This essay examines some limitations of the critical framework deployed by theorists of modern secular Punjabi literature to establish the distinct of this genre and the nature of secular poetic consciousness in contradistinction from so called “medieval theocentric” literary genres such as gurbāni—better known as Sikh scripture. An important consequence of this reclassification of the “secular modern” versus “medieval sacred” literature, was the de-ontologization of the notion of Word (śabad), achieved by disinvesting the concept of śabad of connection to reality, self and world-making. I offer a different way of reading genres such as gurbāni which not only defy oppositional categories such as premodern/modern, secular/religious, but equally caution us from straightforward identification with the post-secular, post-modern, or post-human.
Religion, secularism, and postsecularism in global south literatures: introduction to the special forum
Authors: Ratti Manav
Published: December 2024

This special forum asks: How is postsecularism shaped by the politics and philosophies of religion, secularism, and postcolonialism? How are the enabling possibilities of postsecularism, combining religion and secularism, explored by writers from the Global South—Africa, Asia, Latin America? Addressing these and other questions, the scholars in this forum examine postcolonial postsecularism across literature, history, criticism, and theory. They study Buddhism, Christianity, Confucianism, Daoism, Hinduism, Islam, and Sikhism. They analyze literary genres and devices that include novels, poetry, scripture, epigraphs, intertexts, and internet fantasy fiction. They critique the work of writers from Algeria, Chile, China, India and its diaspora, Mexico, Tunisia, and Turkey.
Boundary obstacles in social innovation: refugees, volunteers, and caseworkers navigating Denmark’s paradoxical borderscape
Authors: Shapiro Ditte , Kohl Katrine Syppli , Jørgensen Rikke Egaa , Sandberg Marie
Published: December 2024

Collaborative methods have gained traction in migration studies, policy, and practice, in turn, engendering calls for new collaborations between research and practice. Bringing multiple perspectives to the production of knowledge in refugee research is particularly pertinent in Denmark, where incongruent policy aims of integration and of return creates a paradoxical borderscape that refugees, volunteers, and municipal caseworkers must navigate. This article draws on a practice-research project, co-developed by two large civil society organizations and university researchers that included collaborative ethnography among refugees, volunteers, and caseworkers in and around a social innovation initiative. It investigates how the conflicting expectations of integration and return shape efforts to change social relationships and strengthen the agency of refugees. We approach collaborative efforts from the perspective of boundary work and coin the concept of ‘boundary obstacles’ to describe core challenges to advancing social innovation initiatives with refugees. Building on a thematic analysis of qualitative data comprising fieldnotes and interview transcripts, we identify three boundary obstacles: positionalities, emotionalities, and politicizations. Finally, the article reflects on the prospects and challenges of social innovation and recommends ways to approach those challenges as boundary obstacles that can help set new directions for collaborative research with refugees.
The connections among morphology, environment, and star formation with Galaxy Zoo Hubble
Authors: Ge Xue , Gu Yi-Zhou , Lei Cheng-Long , Zhang Xing-Han
Published: December 2024

Morphology is an important implication for studying the formation and evolution of galaxies. Previous studies have investigated the effects of spiral arms on star formation activities, but it is not clear how clumpy structure affects this process. In this work, we combine Galaxy Zoo Hubble project and 3D-HST/Cosmic Assembly Near-IR Deep Extragalactic Legacy Survey programs to study the influence of morphological structure on star formation processes and the relationship between morphology and the environment at $0 \lt z \lt 1.0$. We find that galaxies with spiral arms and clumpy structures have higher star formation rates than smooth galaxies, and as the redshift decreases, this result remains unchanged. Analysis based on the subsamples, We find that stellar mass is related to the number of arms but not to the number of clumps. In addition, we do not find that an increase in the numbers of arms and/or clumps stimulates greater star formation. We also find that less-clump galaxies preferentially inhabit high-density environments, while more-clump galaxies preferentially inhabit low-density environments. This phenomenon is not significant in spiral galaxies. Our results show that environmental effects may have a greater influence on clumpy structures compared to spiral arm structures, which in turn affects the star formation activities of galaxies.
SIROCCO: a publicly available Monte Carlo ionization and radiative transfer code for astrophysical outflows
Authors: Matthews James H , Long Knox S , Knigge Christian , Sim Stuart A , Parkinson Edward J , Higginbottom Nick , Mangham Samuel W , Scepi Nicolas , Wallis Austen , Hewitt Henrietta A , Mosallanezhad Amin
Published: December 2024

Outflows are critical components of many astrophysical systems, including accreting compact binaries and active galactic nuclei (AGN). These outflows can significantly affect a system’s evolution and alter its observational appearance by reprocessing the radiation produced by the central engine. sirocco (Simulating Ionization and Radiation in Outflows Created by Compact Objects – or ‘the code formerly known as python’) is a Sobolev-based Monte Carlo ionization and radiative transfer code. It is designed to simulate the spectra produced by any system with an azimuthally symmetric outflow, from spherical stellar winds to rotating, biconical accretion disc winds. Wind models can either be parametrized or imported, e.g. from hydrodynamical simulations. The radiation sources include an optically thick accretion disc and various central sources with flexible spectra and geometries. The code tracks the ‘photon packets’ produced by the sources in any given simulation as they traverse and interact with the wind. The code assumes radiative near-equilibrium, so the thermal and ionization state can be determined iteratively from these interactions. Once the physical properties in the wind have converged, sirocco can be used to generate synthetic spectra at a series of observer sightlines. Here, we describe the physical assumptions, operation, performance and limitations of the code. We validate it against tardis, cmfgen, and cloudy, finding good agreement, and present illustrative synthetic spectra from disc winds in cataclysmic variables, tidal disruption events, AGN, and X-ray binaries. sirocco is publicly available on GitHub, alongside its associated data, documentation and sample input files covering a wide range of astrophysical applications.
Numerical modelling of thermal dust polarization from aligned grains in the envelope of evolved stars with updated POLARIS
Authors: Truong Bao , Hoang Thiem , Giang Nguyen Chau , Diep Pham Ngoc , Nguyen Dieu D , Ngoc Nguyen Bich
Published: December 2024

Magnetic fields are thought to influence the formation and evolution of circumstellar envelopes around evolved stars. Thermal dust polarization from aligned grains is a promising tool for probing magnetic fields and dust properties in these environments; however, a quantitative study on the dependence of thermal dust polarization on the physical properties of dust and magnetic fields for these circumstellar environments is still lacking. In this paper, we first perform the numerical modelling of thermal dust polarization in the IK Tau envelope using the magnetically enhanced radiative torque (MRAT) alignment mechanism implemented in our updated POLARIS code, accounting for the effect of grain drift relative to the gas. Despite experiencing grain drift and high gas density $n_{\rm gas} \gt 10^6\, \rm cm^{-3}$, the minimum grain size required for efficient MRAT alignment of silicate grains is $\sim 0.007\!-\!0.05\, \rm \mu m$ due to strong stellar radiation fields. Ordinary paramagnetic grains can achieve perfect alignment by MRAT in the inner envelope of $r \lt 500\, \rm au$ due to stronger magnetic fields of $B\sim 10$ mG–1G, producing the polarization degree of $\sim 10~{{\rm per\ cent}}$. The polarization degree can be enhanced to $\sim 20\!-\!40~{{\rm per\ cent}}$ for superparamagnetic grains with embedded iron inclusions. The magnetic field geometry affects the resulting polarization degree due to the projection effect. We investigate the effect of rotational disruption by RATs (RAT-D) and find that the RAT-D effect decreases the dust polarization degree due to the decrease in the maximum grain size. Our modelling results motivate further observational studies at far-infrared/sub-millimeter to constrain the properties of magnetic fields and dust in evolved star’s envelopes.
ExoMol line lists – LXV. Mid-infrared rovibronic spectroscopy of isotopologues of NiH
Authors: Batrakov Kirill , Yurchenko Sergei N , Owens Alec , Tennyson Jonathan , Mitrushchenkov Alexander , Ross Amanda J , Crozet Patrick , Pashov Asen
Published: December 2024

New line lists for four isotopologues of nickel monohydride, $^{58}$NiH, $^{60}$NiH, $^{62}$NiH, and $^{58}$NiD are presented covering the wavenumber range $\lt 10000$ cm$^{-1}$ ($\lambda \gt 1$ $\mu$m), J up to 37.5 for transitions within and between the three lowest lying electronic states, ${X}\, ^{2}\Delta$, ${W}\, ^{2}\Pi$, and ${V}\, ^{2}\Sigma ^{+}$. The line lists are applicable for temperatures up to 5000 K. The line lists calculations are based on a recent empirical NiH spectroscopic model [Havalyova et al. J. Quant. Spectrosc. Radiat. Transf., 272, 107800, (2021)] which is adapted for the variational nuclear-motion code duo. The model consists of potential energy curves, spin–orbit coupling curves, electronic angular momentum curves, spin-rotation coupling curves, $\Lambda$-doubling correction curve for $^2\Pi$ states and Born–Oppenheimer breakdown (BOB) rotational correction curves. New ab initio dipole moment curves, scaled to match the experimental dipole moment of the ground state, are used to compute Einstein A coefficients. The BYOT line lists are included in the ExoMol data base at www.exomol.com.
A dynamics-based density profile for dark haloes – III. Parameter space
Authors: Diemer Benedikt
Published: December 2024

In the previous paper of this series, we proposed a new function to fit halo density profiles out to large radii. This truncated Einasto profile models the inner, orbiting matter as $\rho _{\rm orb}\propto \exp \left[-2/\alpha \ (r / r_{\rm s})^\alpha - 1/\beta \ (r / r_{\rm t})^\beta \right]$ and the outer, infalling term as a power-law overdensity. In this paper, we analyse the resulting parameter space of scale radius $r_{\rm s}$, truncation radius $r_{\rm t}$, steepening $\alpha$, truncation sharpness $\beta$, infalling normalization $\delta _{\rm 1}$, and infalling slope s. We show that these parameters are non-degenerate in averaged profiles, and that fits to the total profiles generally recover the underlying properties of the orbiting and infalling terms. We study the connection between profile parameters and halo properties such as mass (or peak height) and accretion rate. We find that the commonly cited dependence of $\alpha$ on peak height is an artefact of fitting Einasto profiles to the actual, truncated profiles. In our fits, $\alpha$ is independent of mass but dependent on accretion rate. When fitting individual halo profiles, the parameters exhibit significant scatter but otherwise follow the same trends. We confirm that the entire profiles are sensitive to the accretion history of haloes, and that the two radial scales $r_{\rm s}$ and $r_{\rm t}$ particularly respond to the formation time and recent accretion rate. As a result, $r_{\rm t}$ is a more accurate measure of the accretion rate than the commonly used radius where the density slope is steepest.
Little iLocater: paving the way for iLocater
Authors: Harris Robert J , Crass Jonathan , Johnson Marshall C , Bechter Andrew J , Power Jennifer , Calcines Rosario Ariadna , Crepp Justin R , Bechter Eric B , Sands Brian L , Kopon Derek , Ertel Steve , Barboza Santiago , Bianco Andrea
Published: December 2024

Diffraction-limited radial-velocity instruments offer a pathway towards improved precision and stability, and the exploration of new parameter spaces at high spatial and spectral resolution. However, achieving the necessary performance requires careful instrument design and considerable on-sky testing. We describe the design and construction of ‘Little iLocater’ (Lili), a compact spectrograph that has been used to validate the performance of the front-end fibre-injection system of the iLocater spectrograph. We present the design, assembly, and performance using on-sky data obtained at the Large Binocular Telescope (LBT), including extraction of spectra from standard stars, testing of the atmospheric dispersion corrector to elevations of 40°, and spatially resolved spectra from close companion systems. These results show the front-end fibre-injection system is performing as expected and is indicative of iLocater’s capabilities once installed at the LBT.
Piwi regulates the usage of alternative transcription start sites in the Drosophila ovary
Authors: Chen Jiaying , Liu Na , Qi Hongying , Neuenkirchen Nils , Huang Yuedong , Lin Haifan
Published: December 2024

Alternative transcription initiation, which refers to the transcription of a gene from different transcription start sites (TSSs), is prevalent across metazoans and has important biological functions. Although transcriptional regulation has been extensively studied, the mechanism that selects one TSS over others within a gene remains elusive. Using the Cap Analysis of Gene Expression sequencing (CAGE-seq) method, we discovered that Piwi, an RNA-binding protein, regulates TSS usage in at least 87 genes. In piwi-deficient Drosophila ovaries, these genes displayed significantly altered TSS usage (ATU). The regulation of TSS usage occurred in both germline and somatic cells in ovaries, as well as in cultured ovarian somatic cells (OSCs). Correspondingly, RNA Polymerase II (Pol II) initiation and elongation at the TSSs of ATU genes were affected in germline-piwi-knockdown ovaries and piwi-knockdown OSCs. Furthermore, we identified a Facilitates Chromatin Transcription (FACT) complex component, Ssrp, that is essential for mRNA elongation, as a novel interactor of Piwi in the nucleus. Temporally controlled knockdown of ssrp affected TSS usage in ATU genes, whereas overexpression of ssrp partially rescued the TSS usage of ATU genes in piwi mutant ovaries. Thus, Piwi may interact with Ssrp to regulate TSS usage in Drosophila ovaries by affecting Pol II initiation and elongation.
Structural basis of Cas9 DNA interrogation with a 5′ truncated sgRNA
Authors: Kiernan Kaitlyn A , Kwon Jieun , Merrill Bradley J , Simonović Miljan
Published: December 2024

The efficiency and accuracy of CRISPR-Cas9 targeting varies considerably across genomic targets and remains a persistent issue for using this system in cells. Studies have shown that the use of 5′ truncated single guide RNAs (sgRNAs) can reduce the rate of unwanted off-target recognition while still maintaining on-target specificity. However, it is not well-understood how reducing target complementarity enhances specificity or how truncation past 15 nucleotides (nts) prevents full Cas9 activation without compromising on-target binding. Here, we use biochemistry and cryogenic electron microscopy to investigate Cas9 structure and activity when bound to a 14-nt sgRNA. Our structures reveal that the shortened path of the displaced non-target strand (NTS) sterically occludes docking of the HNH L1 linker and prevents proper positioning of the nuclease domains. We show that cleavage inhibition can be alleviated by either artificially melting the protospacer adjacent motif (PAM)-distal duplex or providing a supercoiled substrate. Even though Cas9 forms a stable complex with its target, we find that plasmid cleavage is ∼1000-fold slower with a 14-nt sgRNA than with a full-length 20-nt sgRNA. Our results provide a structural basis for Cas9 target binding with 5′ truncated sgRNAs and underline the importance of PAM-distal NTS availability in promoting Cas9 activation.
Exploring the diversity of anti-defense systems across prokaryotes, phages and mobile genetic elements
Authors: Tesson Florian , Huiting Erin , Wei Linlin , Ren Jie , Johnson Matthew , Planel Rémi , Cury Jean , Feng Yue , Bondy-Denomy Joseph , Bernheim Aude
Published: December 2024

The co-evolution of prokaryotes, phages and mobile genetic elements (MGEs) has driven the diversification of defense and anti-defense systems alike. Anti-defense proteins have diverse functional domains, sequences and are typically small, creating a challenge to detect anti-defense homologs across prokaryotic and phage genomes. To date, no tools comprehensively annotate anti-defense proteins within a desired sequence. Here, we developed ‘AntiDefenseFinder’—a free open-source tool and web service that detects 156 anti-defense systems of one or more proteins in any genomic sequence. Using this dataset, we identified 47 981 anti-defense systems distributed across prokaryotes and their viruses. We found that some genes co-localize in ‘anti-defense islands’, including Escherichia coli T4 and Lambda phages, although many appear standalone. Eighty-nine per cent anti-defense systems localize only or preferentially in MGE. However, >80% of anti-Pycsar protein 1 (Apyc1) resides in nonmobile regions of bacterial genomes. Evolutionary analysis and biochemical experiments revealed that Apyc1 likely originated in bacteria to regulate cyclic nucleotide (cNMP) signaling, but phage co-opted Apyc1 to overcome cNMP-utilizing defenses. With the AntiDefenseFinder tool, we hope to facilitate the identification of the full repertoire of anti-defense systems in MGEs, the discovery of new protein functions and a deeper understanding of host–pathogen arms race.
Trypanosoma cruzi eIF4E3- and eIF4E4-containing complexes bind different mRNAs and may sequester inactive mRNAs during nutritional stress
Authors: Gabiatti Bernardo Papini , Freire Eden Ribeiro , Ferreira da Costa Jimena , Ferrarini Mariana Galvão , Reichert Assunção de Matos Tatiana , Preti Henrique , Munhoz da Rocha Isadora , Guimarães Beatriz Gomes , Kramer Susanne , Zanchin Nilson Ivo Tonin , Holetz Fabíola Barbieri
Published: December 2024

Many eIF4F and poly(A)-binding protein (PABP) paralogues are found in trypanosomes: six eIF4E, five eIF4G, one eIF4A and two PABPs. They are expressed simultaneously and assemble into different complexes, contrasting the situation in metazoans that use distinct complexes in different cell types/developmental stages. Each eIF4F complex has its own proteins, messenger RNAs (mRNAs) and, consequently, a distinct function. We set out to study the function and regulation of the two eIF4F complexes of the parasite Trypanosoma cruzi and identified the associated proteins and mRNAs of eIF4E3 and eIF4E4 in cells in exponential growth and in nutritional stress, an inducer of differentiation to an infective stage. Upon stress, eIF4G and PABP remain associated with the eIF4E, but the associations with other 43S pre-initiation factors decrease, indicating ribosome attachment is impaired. Most eIF4E3-associated mRNAs encode for proteins involved in anabolic metabolism, while eIF4E4 associate with mRNAs encoding ribosomal proteins as in Trypanosoma brucei. Interestingly, for both eIF4E3/4, more mRNAs were associated in stressed cells than in non-stressed cells, even though these have lower translational efficiencies in stress. In summary, trypanosomes have two co-existing eIF4F complexes associating to different mRNAs, but not stress/differentiation-associated mRNAs. Under stress, both complexes exit translation but remain bound to their mRNA targets
BASAL: a universal mapping algorithm for nucleotide base-conversion sequencing
Authors: Xu Moping , Liu Xiaoyang , Wang Miao , Luo Tingting , Gao Yawei , Liu Jun , Shi Jiejun
Published: December 2024

Utilizing base-conversion (BC) techniques, single-base resolution profiling of RNA and DNA modifications has significantly advanced. BC strategies range from one-way conversions (e.g. cytosine-to-thymine for 5-methylcytosine, adenine-to-guanine for N6-methyladenosine), to multi-way conversions (e.g. adenine to cytosine/guanine/thymine for N1-methyladenosine) and deletion-induced conversions (e.g. pseudouridine-to-deletion). Existing sequence aligners struggle with these diverse conversions, often leading to misaligning or inefficiency. We introduce BASAL (BAse-conversion Sequencing ALigner), which leverages bit-masking technology to accurately calculate mismatch penalties and supports all BC strategies. BASAL outperforms state-of-the-art tools in both mapping accuracy and efficiency. Through simulated and real data testing, along with experimental validation, we demonstrate that BASAL excels at identifying reliable modification sites. Moreover, BASAL enhances single-cell m6A analysis, revealing cell subpopulations and a cell evolutionary direction that align with biological functions, which other aligners fall short. BASAL’s versatility establishes it as a universal aligner for RNA and DNA modification sequencing, facilitating groundbreaking discoveries in epigenomics and epitranscriptomics.
Novel BRCA1–PLK1–CIP2A axis orchestrates homologous recombination-mediated DNA repair to maintain chromosome integrity during oocyte meiosis
Authors: Lee Crystal , Oh Jeong Su
Published: December 2024

Double-strand breaks (DSBs) are a formidable threat to genome integrity, potentially leading to cancer and various genetic diseases. The prolonged lifespan of mammalian oocytes increases their susceptibility to DNA damage over time. While somatic cells suppress DSB repair during mitosis, oocytes exhibit a remarkable capacity to repair DSBs during meiotic maturation. However, the precise mechanisms underlying DSB repair in oocytes remain poorly understood. Here, we describe the pivotal role of the BRCA1–PLK1–CIP2A axis in safeguarding genomic integrity during meiotic maturation in oocytes. We found that inhibition of homologous recombination (HR) severely impaired chromosome integrity by generating chromosome fragments during meiotic maturation. Notably, HR inhibition impaired the recruitment of CIP2A to damaged chromosomes, and the depletion of CIP2A led to chromosome fragmentation following DSB induction. Moreover, BRCA1 depletion impaired chromosomal recruitment of CIP2A, but not vice versa. Importantly, the impaired chromosomal recruitment of CIP2A could be rescued by PLK1 inhibition. Consequently, our findings not only underscore the importance of the chromosomal recruitment of CIP2A in preventing chromosome fragmentation, but also demonstrate the regulatory role of the BRCA1–PLK1–CIP2A axis in this process during oocyte meiotic maturation.