bluuebunny/crossref_metadata_2025_split huggingface dataset:
MIP4IBD: An Easy and Rapid Genotyping-by-Sequencing Assay for the Inflammatory Bowel Diseases Risk Loci
Authors: Verstockt Sare , Hannes Laurens , Jans Deborah Sarah , Deman Stephanie , Souche Erika , van der Werf Ilse , Vandermeulen Liv , Lobaton Triana , Laukens Debby , Verstockt Bram , Van Houdt Jeroen , Hoischen Alexander , Vermeire Séverine , Cleynen Isabelle 
Published: December 2024

Abstract

Background
Inflammatory bowel diseases (IBD) are polygenic, with many genetic variants contributing to disease risk. Knowing the genotype of specific variants or calculating a combined genetic risk score benefits translational and functional research. To address this, we developed MIP4IBD, a flexible and cost-effective genotyping-by-sequencing assay using molecular inversion probes (MIPs).

Methods
The assay targets 463 IBD risk variants, and 77 additional relevant variants. Molecular inversion probes capture and library preparation were optimized using 15 IBD DNA samples, comparing genotypes with immunochip. A custom GitHub pipeline was created for data processing, performance testing, and genotype calling. The final design was validated on a larger scale (149 IBD patients, 104 non-IBD controls, and 3 external cell lines), incorporating post hoc quality control criteria.

Results
The assay achieved a 3.5-day turnaround time at €15 per sample with optimal sample throughput, demonstrating a 92.6% success rate in variant capture and genotype concordance rates of 99.3% and 99.6% with Infinium Global Screening Array24 BeadChip and WGS, respectively. A downstream application involved the calculation of a weighted IBD polygenic risk score (PRS), which was significantly higher in IBD patients than controls (mean 0.42 vs −0.49, P = 1.95E−11). Individuals in the highest PRS quartile had a 15.7-fold (95% CI: 6.5-38.3) risk of developing IBD and an earlier age of onset (26 vs 37 years, P = 0.02), compared to the lowest quartile.

Conclusions
MIP4IBD is a validated, scalable genotyping assay targeting IBD risk loci, with an integrated bioinformatics pipeline from sequencing data to genotypes and PRS calculation. Its cost-effectiveness and flexibility for additional variants make it particularly appealing for translational and clinical applications.
Research on the mechanism of green industry investment to promote sustainable utilization of water resources
Authors: Jiang Juan 
Published: December 2024

Abstract
This study aims to deeply analyze how green industry investment can effectively promote the sustainable utilization of water resources. Firstly, we defined the concept, characteristics, and corresponding evaluation index system of green industry investment. Subsequently, through the comprehensive application of literature review, theoretical analysis, and empirical case analysis, we constructed a mechanism model to reveal the promoting effect of green industry investment on the sustainable use of water resources and verified it with relevant data. Meanwhile, this study emphasizes the critical roles of policies, technologies, and markets in the sustainable utilization of water resources. The empirical results indicate that investment in green industries has improved water resource utilization efficiency and strengthened water resource protection. Therefore, the policy recommendations proposed in this study have high practical significance for guiding the practice of green industry investment and sustainable water resource utilization in China.
COVID-19 Pandemic, Poverty and Health Outcomes in South Africa: Do Social Protection Programmes Protect?
Authors: Omotayo Abiodun Olusola , Ogunniyi Adebayo Isaiah 
Published: December 2024

Abstract
The COVID-19 pandemic resulted in significant income loss for many people and deepened poverty for individuals and vulnerable populations who were adversely affected through job losses. In South Africa, income loss made it harder to acquire health care and a healthy food, which had a negative impact on health outcomes. This study hypothesised that the COVID-19 shocks disproportionately affects the poor's health, hence the need to know the impact of social protection programmes and interventions through the South Africa Social Security Grant (SASSG). Herewith, we employed the nationally represented, robust and reliable National Income Dynamics Study (NIDS) data set which was conducted in 2017 (pre-COVID-19), with the first wave of the NIDS-Coronavirus Rapid Mobile Survey (NIDS-CRAM) conducted in 2021 (during COVID-19). The household's per capita total income was used to generate poverty lines, while concentration curves and indices were employed to explain the income-health inequalities. The difference-in-difference with fixed effects model was used to estimate the impact of SASSG on the COVID-19 poverty stressors and self-reported health status. Given the significance and magnitude of institutional variables in determining the socio-economic inequalities in poor health, addressing hunger, income inequality and unemployment slightly helped to mitigate income-health inequalities during the COVID-19 shocks. We found that the social protection intervention in South Africa (SASSG) cushioned the impact of the COVID-19 pandemic in the context of poverty stressors and self-reported health status. Therefore, we advocate for programmes in South Africa that focus on reducing poverty and health disparities connected to income, as well as more proactive social protection programmes.
Coping Strategies and Inequalities during the COVID-19 Pandemic Period: Evidence from Kenya
Authors: Giovanis Eleftherios , Ozdamar Oznur 
Published: December 2024

Abstract
Governments worldwide have implemented stringent lockdown measures in response to the COVID-19 pandemic outbreak, which had an adverse impact on employment, affecting people's public life, health and well-being. People have witnessed job losses, cuts in wages and a decline in their living standards. This study aims to estimate the inequalities and well-being costs, demonstrating the living standards necessary to make up for people's wage reduction or job losses. In particular, we aim to explore the coping strategies used to enhance their well-being compared to those of households without a coping strategy. We use food insecurity as a measure of well-being outcome. The empirical analysis relies on detailed household surveys from the World Bank Microdata Library. We use seven waves of the Panel COVID-19 Rapid Response Phone Survey with Households in 2020–2022 in Kenya. Also, the results highlight the potential inequalities of the COVID-19 pandemic across gender and types of workers, such as those employed in the informal sector and on temporary contracts. The findings show that specific coping strategies, such as delayed payment obligations, credit purchases and reduced non-food consumption, are associated with larger inequalities. Regarding the gender of the head of the household, the results suggest that the disparities between female-headed households that had to cope with income and employment loss and female-headed households that did not require to follow any strategy are significantly higher compared to their male counterparts. We derive similar concluding remarks when we consider households with social security coverage and the type of employment contract.
Characterization of UGT8 as a monogalactosyl diacylglycerol synthase in mammals
Authors: Ohba Yohsuke , Motohashi Mizuki , Arita Makoto 
Published: December 2024

Abstract
Monogalactosyl diacylglycerol (MGDG) is a major membrane lipid component in plants and is crucial for proper thylakoid functioning. However, MGDG in mammals has not received much attention, partly because of its relative scarcity in mammalian tissues. In addition, the biosynthetic pathway of MGDG in mammals has not been thoroughly analysed, although some reports have suggested that UGT8, a ceramide galactosyltransferase, has the potential to catalyse MGDG biosynthesis. Here, we successfully captured the endogenous levels of MGDG in HeLa cells using liquid chromatography quadrupole time-of-flight mass spectrometry (LC–QTOF-MS)-based lipidomics. Cellular MGDG was completely depleted in CRISPR/Cas9-mediated UGT8 knockout (KO) HeLa cells. Transient overexpression of UGT8 enhanced MGDG production in HeLa cells, and the corresponding cell lysates displayed MGDG biosynthetic activity in vitro. Site-directed mutagenesis revealed that His358 within the UGT signature sequence was important for its activity. UGT8 was localized in the endoplasmic reticulum and activation of the unfolded protein response by membrane lipid saturation was impaired in UGT8 KO cells. These results demonstrate that UGT8 is an MGDG synthase in mammals and that UGT8 regulates membrane lipid saturation signals in cells.
Host control by Acmispon strigosus constrains fitness gains of ineffective Bradyrhizobium symbionts in mixed infections
Authors: Wendlandt Camille E , Avelar-Barragan Julio , Zomorrodian Avissa J , Al-Moussawi Khadija , Porter Stephanie S , Sachs Joel L 
Published: December 2024

Abstract
Plant hosts can gain significant growth benefits from symbiosis with microbes, but these benefits could be threatened by divergent fitness interests among partners. Here, we measured fitness outcomes in symbiosis, by varying the genotypes of both microbes and hosts, to examine scenarios that might favour uncooperative symbionts. We studied associations between Acmispon strigosus, an annual legume native to California, and its nitrogen-fixing symbionts in the genus Bradyrhizobium. Bradyrhizobium symbionts form root nodules on compatible hosts, with strains varying from effective, fixing substantial nitrogen for the host, to ineffective strains that do not fix nitrogen and provide no benefit to host growth. We co-inoculated four A. strigosus plant lines with nine combinations of effective and ineffective Bradyrhizobium strains and measured the relative fitness of ineffective strains within individual nodules, as hosts must select against uncooperative symbionts to maintain benefits. In mixed infections, ineffective strains always had lower relative fitness in nodules compared to beneficial strains, consistent with efficient punishment of non-fixing rhizobia. However, ineffective strains exhibited genotypic variation in their fitness in nodules within individual nodules co-infected with a beneficial strain, suggesting a role for symbiont competitiveness in shaping this joint phenotype. Variation in symbiont fitness during co-inoculations did not measurably affect plant performance, suggesting that predicted conflict over the joint phenotype of rhizobia fitness has negligible effect on the host.
Genome assembly of the winter ant, Prenolepis imparis
Authors: Cash Elizabeth I , Ward Philip S , Escalona Merly , Sahasrabudhe Ruta , Miller Courtney , Toffelmier Erin , Fairbairn Colin , Seligmann William , Shaffer H Bradley , Tsutsui Neil D 
Published: December 2024

Abstract
The winter ant, Prenolepis imparis, is one of the most common, widespread, and conspicuous ant species in North America. P. imparis is well adapted to cold climates, and consequently, is often noted as the only active ant species during colder months. This specialized life history makes P. imparis a useful model organism for exploring thermal physiology and understanding the potential impacts of a warming climate on insects. Phylogeographic studies have revealed deeply divergent lineages across North America, as well as a single collection of an apparent social parasite in California. In light of its distinctive cold adaptation and recently discovered geographic diversity, a better understanding of the underlying genetic patterns of the winter ant is valuable to future conservation efforts for this species. Here, we present a high-quality genome assembly of P. imparis from Santa Clara County, California. This genome assembly consists of 787 scaffolds spanning 327.3 Mb, with contig N50 of 901.9 kb, scaffold N50 of 18.7 Mb, and BUSCO completeness of 96.5%. This genome assembly provides an essential foundation for future studies of the winter ant and will be particularly useful for understanding the genetic basis of thermal adaptation, cold resistance, chemical ecology, and the resilience of organisms in response to a changing climate.
Natural history of HPV-16 E6 serology among cancer-free men in a multicenter longitudinal cohort study
Authors: Shing Jaimie Z , Giuliano Anna R , Brenner Nicole , Michels Birgitta , Hildesheim Allan , Srivastava Sudhir , Sirak Bradley A , Schussler John , Liu Danping , Wang Wendy , Waterboer Tim , Kreimer Aimée R 
Published: December 2024

Abstract

Background
Human papillomavirus (HPV) type 16 E6 protein seropositivity accurately predicts oropharyngeal squamous cell carcinoma risk decades before diagnosis; but the biomarker’s translational potential is unknown. To inform considerations for oropharyngeal squamous cell carcinoma screening, we described HPV-16 E6 seroprevalence, predictors, and kinetics among cancer-free men.

Methods
In a cohort study in Brazil, Mexico, and the United States, we calculated HPV-16 E6 seropositivity (median fluorescence intensity &gt; 1000), measured by multiplex serology, in cancer-free men. We assessed HPV-16 E6 seropositivity predictors using logistic regression, adjusting for country, age, sexual orientation, and lifetime number of sexual partners. Among HPV-16 E6 seropositive men, we retrieved all available retrospective serum samples and described temporal HPV-16 E6 antibody patterns.

Results
Of 3997 men, 14 had HPV-16 E6 antibodies detected (seroprevalence = 0.35%, 95% CI = 0.19% to 0.59%; median fluorescence intensity = 2407 [IQR = 1325-5986]). Older age was associated with increased odds of HPV-16 E6 seropositivity (50-84 years vs 18-29 years odds ratio = 16.61, 95% CI = 2.20 to 417.03). Serum from 11 of the 14 seropositive men retested positive; 6 men had median fluorescence intensity above 5000, of whom 2 had median fluorescence intensity greater than 10 000. Seven men had 3 or more years of follow-up; all were persistently seropositive for 3 years. One man was seropositive for 9 years but seroreverted at his exit visit. Oral HPV-16 DNA (prevalence = 1.13%) was associated with HPV-16 E6 seropositivity (odds ratio = 16.87, 95% CI = 3.35 to 69.55), but oral HPV-16 DNA positivity was not persistent over follow-up, even when HPV-16 E6 antibodies were persistently detected.

Conclusion
Although HPV-16 E6 seropositivity is rare, it is generally stable once detected; thus, HPV-16 E6 antibodies may be an informative biomarker of HPV-driven oropharyngeal squamous cell carcinoma. Few men seroreverted following HPV-16 E6 seropositivity but remained close to the seropositivity cutoff; thus, cancer risk among these men is less clear.
(154) MEN’S HEALTH AND THE LITIGIOUS PATIENT: A REVIEW OF MALPRACTICE CASES
Authors: Voleti S , Warren C , Ghaith S , Punjani N 
Published: December 2024

Abstract

Introduction
Recent literature suggests growing rates of malpractice claims against Urologists, with the incidence of being sued seeming to be unrelated to one’s professional reputation. These cases provide insight into errors that may lead to litigation. Given national trends of rising malpractice cases, estimates that a Urologist can expect to be sued at least twice in their careers are likely underestimates. Malpractice cases can give insight into the common medical errors rising to the level of litigation. Given the elective nature of procedures within sexual medicine, understanding litigation related to these cases is crucial.

Objective
We aim to analyze malpractice suits related to men’s health and highlight clinical presentations and legal outcomes.

Methods
Per STROBE guidelines, we searched the publicly available Thomson Reuters Westlaw legal database for “jury verdicts and settlements” from January 1970 to August 2023 to identify medical malpractice cases in Urology. Patient demographics, clinical presentation, alleged error, and legal outcomes were abstracted during full case review by an independent screener. Cases related to men’s sexual health or fertility that named a urologist as the defendant were fully analyzed.

Results
A total of 553 Urology cases were extracted, with 23 men’s health related cases subsequently analyzed and summarized in Table 1. The most common conditions associated with litigation were erectile dysfunction (penile prosthesis) (39%), epidydimal pathology (13%), and varicocele (13%). The most common allegations were misdiagnosis (26%), surgical complication (22%), lack of informed consent (22%), and violation of standard of care (22%). Of the 23 cases, 57% ruled “no liability” in favor of the urologist, 39% ruled in favor of the plaintiff with a median award of $335,000 (IQR = 100,000-450,000), and one was settled for $316,338. Among cases ruled as negligent, performing the incorrect procedure, surgical complications, and violating the standard of care were prominent allegations. Florida (26%) and Pennsylvania (17%) had the most cases in this sample. Of note, there were no cases for penile plication, plaque excision, microsurgical cord denervation, vasectomy reversal, or sperm retrieval, and only one for vasectomy.

Conclusions
This study characterizes malpractice cases related to men’s sexual health naming urologists as defendants. Despite fear of litigation, this review of the Westlaw database revealed only 23 cases related to men’s health since 1970. Moreover, the majority of cases ruled in favor of the Urologist. Obtaining comprehensive informed consent, following national guidelines, and responding appropriately to surgical complications may minimize likelihood of litigation and maximize patient outcomes.

Disclosure
No.
(155) IT CAN ONLY GET WORSE: AN ANALYSIS OF FACTORS IMPACTING ONLINE PHYSICIAN REVIEWS
Authors: Miller J , Ahmed Z , Hammad M , Gryzinski G , Chawareb E , Yafi F 
Published: December 2024

Abstract

Introduction
Physician review websites offer patients insight to their potential care teams when seeking a new provider. A firm understanding of the factors which patients deem important when assigning these ratings may allow sexual medicine providers an opportunity to improve patient satisfaction.

Objective
To analyze the impact of commonly cited positive and negative qualities of a sexual medicine providers’ practice on online provider ratings.

Methods
Online ratings and reviews through Healthgrade.com and Vitals.com were collected for all physicians listed in the SMSNA Healthcare Provider Directory. Physicians were included if they had received more than 10 ratings and 5 written reviews. The frequency for which specific positive and negative descriptors were included in written reviews was compared to a provider’s average online rating using Wilcoxon-Mann–Whitney tests and non-parametric correlation. Factors which were significantly associated with changes in average ratings were then tested using multiple regression.

Results
Of 331 SMSNA providers, 145 (43.8%) met the inclusion criteria, including 129 male and 16 female providers, receiving an average of 57.0 ratings and 22.6 written reviews each. The average rating was 3.96/5. Factors significantly associated with worsened online ratings included physicians appearing rude or uncaring (-47.0%, p = 0.013), poor clinic staff or nurse quality (-39.2%, p = 0.000), lack of email or phone availability (-37.2%, p = 0.001), poor facilities appearance (-29.5%, p = 0.045), and complications following procedures (-22.7%, p = 0.028). No factors were significantly associated with improved rating scores (Table 1).

Conclusions
Physicians can gain insight to the patient perspective through a careful review of common trends in online physician reviews. On an analysis of reviews for SMSNA providers, multiple factors which remain in the provider’s control, including appearing caring to patients, quality of clinic staff or nurses, and availability by phone or email, appeared to significantly impact online ratings. By focusing on these factors, sexual medicine providers may be able to maintain positive online reviews while offsetting the impact of factors that may remain outside of their control, including the quality of clinic or hospital facilities and complications following procedures. Despite frequent emphasis, wait times and cost of care did not appear to impact overall ratings.

Disclosure
Any of the authors act as a consultant, employee or shareholder of an industry for: Coloplast.
(173) SINGLE SURGEON EXPERIENCE WITH RESERVOIR PLACEMENT DURING PENOSCROTAL INFLATABLE PENILE IMPLANT SURGERY, IS A COUNTER INCISION NECESSARY
Authors: Gheiler E 
Published: December 2024

Abstract

Introduction
Reservoir placement during penoscrotal inflatable penile implant surgery (IPP) can be done via the primary incision or through a separate lower abdominal incision. Surgeons that do routine secondary incisions state risks of vascular, bowel or bladder injury. There is a distinct advantage in avoiding a secondary incision in terms of pain, added surgical times and possible wound infections.

Objective
I decided to review my cases over the last several years to determine the number of times a counter incision was necessary and to determine the true incidence of such stated risk factors. To help young surgeons determine the risks of reservoir placement in a real-world experience.

Methods
IPP done between 2008 and 2023 were retrospectively reviewed to determine frequency of counter incision and rates of complications due to reservoir placement. All IPP were performed by a single surgeon utilizing the penoscrotal approach.

Results
A total of 4,589 IPP were performed, 4223 Virgin and 366 removal and replacement. The first 3778 cases had the reservoir placed in the space of Retzius the next 611 done ectopically and the last 200 by a medially placed submuscular approach. One (0.02%) case of bladder injury was identified in the early ectopic experience, treated with catheter placement and contralateral reservoir placement. In 8 (0.17%) patients the reservoir herniated and needed replacement. None in the new approach. No cases of bowel or vascular injury were encountered. New reservoir placement technique is achieved in less than 1 minute. None of the cases required a counter incision.

Conclusions
Reservoir placement during penoscrotal IPP without a counter incision, is an extremely safe and efficient technique. We should encourage the new generation implanters to properly learn this approach and not scare them with rarely seen potential complications.

Disclosure
Any of the authors act as a consultant, employee or shareholder of an industry for: Boston Scientific.