bluuebunny/crossref_metadata_2025 huggingface dataset:
One survey fits all? Evaluating the relevance of sexual function measures designed for cis women in trans women postvaginoplasty
Authors: Fraiman Elad , Goldblatt Carly , Loria Matthew , Mishra Kirtishri , Pope Rachel
Published: July 2023

Background

Providers are currently using surveys designed for cisgender women and/or creating their own questionnaires to evaluate the sexual function and satisfaction (SFS) of transgender women postvaginoplasty (TWPV), despite the marked difference in anatomy and lived experience between these groups.

Aim

To evaluate the appropriateness of the current assays that have been validated in cisgender women and to assess their applicability in studying SFS in TWPV.

Methods

Surveys assessing female SFS that were validated in English speakers in North America were compiled and reviewed. Percentages reflect the proportion of surveys that asked questions deemed relevant or irrelevant for TWPV. Assessed variables included questions about endogenous lubrication, pain/discomfort with penetration, and other sexual activity.

Outcomes

Outcomes of interest were questions that fell into 1 of 2 categories: questions irrelevant to TWPV (present/irrelevant) and those relevant for TWPV (present/relevant).

Results

All surveys contained present/irrelevant questions. Endogenous lubrication—a property of the natal vagina that may not be present in the neovagina—was the primary present/irrelevant question and was asked in 69.2% of the surveys. Vaginal pain, a present/relevant question, was assessed in 46.2% of surveys. Furthermore, questions requiring a partnered relationship to answer were asked in 61.5% of surveys, which may detract from the assessment of SFS in individuals who do not have sexual partners. Notably, there was also a lack of questions important for evaluating SFS in TWPV, such as assessing satisfaction of the caliber and depth of the neovagina, erogenous stimulation of the prostate during insertive intercourse, and cosmetic appearance of the vulva.

Clinical Implications

This analysis raises concerns about the clinician’s ability to meaningfully assess SFS in TWPV using the tools available.

Strengths and Limitations

This article is the first of its kind to qualitatively assess the applicability of currently validated SFS questionnaires in TWPV. Limitations include the inability to draw definitive conclusions due to the qualitative nature of the study and the possibility of missing complex biopsychosocial factors, as trans individuals were not directly involved in the assessments of applicability.

Conclusion

Given that the existing surveys are not designed to assess the SFS of TWPV, we call for the development of a validated survey for this population, which is in line with the precedent set by several other questionnaires validated for similarly specific populations.
Hexachordal Solmization and Syllable-Invariant Counterpoint in the Vocal Music of William Byrd
Authors: Long Megan Kaes
Published: July 2023

William Byrd was an unusually creative contrapuntist: he is known for his virtuosic double counterpoint, his expressive manipulation of soggetti (imitative subjects), his capacity for exhausting possible contrapuntal combinations in stretto passages, and his points of imitation that build toward an expressive climax (what Joseph Kerman [1981] has described as Byrd’s “cumulative” imitation). This article addresses a cumulative technique that has not previously been identified: syllable-invariant counterpoint. Byrd often develops points of imitation where the soggetto is solmized identically in two hexachords (what sixteenth-century theorists called fuga, in contrast to imitazione). But Byrd frequently builds points toward an extra statement of the soggetto in a new, bonus hexachord; this transposition introduces a new semitone foreign to the work’s local tonality. Byrd thematizes syllable invariance throughout his vocal repertory, particularly in his serious motets. This article shows how Byrd combines syllable-invariant counterpoint with a variety of distinct imitative strategies to achieve specific expressive and tonal goals. The article further considers the implications of syllable invariance for tonal structure in Byrd’s music. Syllable-invariant counterpoint makes visible the constraints and affordances of Byrd’s tonal system, the Guidonian diatonic gamut under hexachordal solmization. Byrd carefully controlled the tonal compass of his works by using syllable invariance, among other strategies, to manipulate his counterpoint’s “chromatic” ambit. Syllable-invariant counterpoint—which Renaissance musicians would have understood as a diatonic, not chromatic, strategy—encompasses Byrd’s contrapuntal, expressive, and tonal compositional techniques.
Epidemiology and Antimicrobial Resistance of Campylobacter Infections in the United States, 2005–2018
Authors: Ford Laura , Healy Jessica M , Cui Zhaohui , Ahart Lauren , Medalla Felicita , Ray Logan C , Reynolds Jared , Laughlin Mark E , Vugia Duc J , Hanna Samir , Bennett Christy , Chen Jessica , Rose Erica Billig , Bruce Beau B , Payne Daniel C , Francois Watkins Louise K
Published: July 2023

Background

Campylobacter is the most common cause of bacterial diarrhea in the United States; resistance to macrolides and fluoroquinolones limits treatment options. We examined the epidemiology of US Campylobacter infections and changes in resistance over time.

Methods

The Foodborne Diseases Active Surveillance Network receives information on laboratory-confirmed Campylobacter cases from 10 US sites, and the National Antimicrobial Resistance Monitoring System receives a subset of isolates from these cases for antimicrobial susceptibility testing. We estimated trends in incidence of Campylobacter infection, adjusting for sex, age, and surveillance changes attributable to culture-independent diagnostic tests. We compared percentages of isolates resistant to erythromycin or ciprofloxacin during 2005–2016 with 2017–2018 and used multivariable logistic regression to examine the association of international travel with resistance.

Results

Adjusted Campylobacter incidence remained stable or decreased for all groups analyzed since 2012. Among 2449 linked records in 2017–2018, the median patient age was 40.2 years (interquartile range, 21.6–57.8 years), 54.8% of patients were male, 17.2% were hospitalized, and 0.2% died. The percentage of resistant infections increased from 24.5% in 2005–2016 to 29.7% in 2017–2018 for ciprofloxacin (P < .001) and from 2.6% to 3.3% for erythromycin (P = .04). Persons with recent international travel had higher odds than nontravelers of having isolates resistant to ciprofloxacin (adjusted odds ratio [aOR] varied from 1.7 to 10.6 by race/ethnicity) and erythromycin (aOR = 1.7; 95% confidence interval, 1.3–2.1).

Conclusions

Campylobacter incidence has remained stable or decreased, whereas resistance to antimicrobials recommended for treatment has increased. Recent international travel increased the risk of resistance.
Concurrent Sexually Transmitted Infection Testing Among Patients Tested for Mpox at a Tertiary Healthcare System
Authors: Mourad Ahmad , Alavian Naseem , Woodhouse Edwin W , Niehaus Emily , Cunningham Hayley , Zavala Sofia , Kohler Patricia , Pappas Steven , Yarrington Michael , Okeke Nwora Lance , Wolfe Cameron R , Cox Gary M , Dicks Kristen V , Stout Jason E
Published: July 2023

Coinfection with sexually transmitted infections (STIs) and mpox is common. We evaluated concurrent STI testing among Duke Health patients tested for mpox. We found that most patients tested for mpox were not comprehensively tested for STIs, despite concurrent STIs being diagnosed in 15% of patients when testing was performed.
The Role of Religion in Domestic Violence and Abuse in UK Muslim Communities
Authors: Chowdhury Rahmanara
Published: July 2023

Existing research on the role of faith in the aftermath of domestic violence and abuse (DVA) often fails to adequately situate the role played by religion throughout the DVA trajectory. This article draws on qualitative research conducted with 10 Muslim female survivors and 9 professionals providing support in DVA cases to investigate the nature, occurrence, and impact of DVA within Muslim religious communities. This article specifically explores the role of religion at four levels; individual psycho-social-spiritual level, the level of additional stakeholders, within the context of intersectionality, and at a macro-societal level. It is argued that religion and practice of faith plays a nuanced role at each of these levels. The research found that holistic approaches to faith resulted in faith manifesting as an empowering resource for DVA survivors. Reductionist and androcentric approaches to faith however resulted in the enabling and continuation of abuse and abusive structures. Findings indicate the need for service provision to provide tailored and culturally informed support to Muslim clients, particularly in relation to faith. The web model of DVA provides a structured framework through which this can be achieved.
Using foraging range and colony size to assess the vulnerability of breeding seabirds to oil across regions lacking at-sea distribution data
Authors: O’Hanlon Nina J , Bond Alexander L , Masden Elizabeth A , Boertmann David , Bregnballe Thomas , Danielsen Jóhannis , Descamps Sébastien , Petersen Aevar , Strøm Hallvard , Systad Geir , James Neil A
Published: July 2023

With the projected increases in shipping activity and hydrocarbon extraction globally, there is an increased risk of negative ecological impacts from oil pollution on the marine environment, including seabirds. Oil Vulnerability Indices (OVIs) are a common approach to assess seabird species vulnerability to oil pollution and to identify where species are most at risk, typically across regional spatial scales and for a relatively limited number of species. This approach generally requires comprehensive data on at-sea distributions and densities; however, for many regions, these data are limited. We present a simplified OVI to assess seabird species vulnerability to oil pollution. To create the spatial component of the OVI, we used a predictive foraging radius approach, using existing colony size and foraging range data, to project at-sea distributions of seabird populations during the breeding season. We demonstrate this approach over a large spatial scale, the eastern North Atlantic, which includes areas where seabird at-sea data are lacking. Our results reveal areas off west Greenland, Iceland, and Norway where seabirds are most vulnerable to oil pollution during the breeding season, largely driven by large colonies of auks (Alcidae). We also identify locations along the coast of mainland Norway, Iceland, and Scotland, where seabirds are particularly at risk to oil pollution associated with major shipping routes. Identifying areas where species are most at risk can help inform where, and which, measures should be put in place to mitigate the impacts of oil pollution, such as protecting and avoiding high risk areas, for example, through adopting dynamic Areas to be Avoided (ATBAs). Our simplified OVI combined with the predictive foraging radius approach can be adapted to other regions globally that lack seabird-at-sea distribution data, to other marine wildlife, and to assess risk from hydrocarbon extraction and other anthropogenic threats, including fishing activities and offshore renewable developments.
Co-evolution of dust grains and protoplanetary disks
Authors: Tsukamoto Yusuke , Machida Masahiro N , Inutsuka Shu-ichiro
Published: July 2023

We propose a new evolutionary process for protoplanetary disks, the co-evolution of dust grains and protoplanetary disks, revealed by dust–gas two-fluid non-ideal magnetohydrodynamics simulations considering the growth of dust grains and associated changes in magnetic resistivity. We found that the dust growth significantly affects disk evolution by changing the coupling between the gas and the magnetic field. Moreover, once the dust grains grow sufficiently large and the adsorption of charged particles on to them becomes negligible, the physical quantities (e.g., density and magnetic field) of the disk are well described by characteristic power laws. In this disk structure, the radial profile of density is steeper and the disk mass is smaller than those of the model ignoring dust growth. We analytically derive these power laws from the basic equations of non-ideal magnetohydrodynamics. The analytical power laws are determined only by observable physical quantities, e.g., central stellar mass and mass accretion rate, and do not include difficult-to-determine parameters, e.g., the viscous parameter α. Therefore, our model is observationally testable and this disk structure is expected to provide a new perspective for future studies on protostar and disk evolution.
Parents’ experiences of their children’s medical journeys with tracheostomies: A Focus Group Study
Authors: Castro-Codesal Maria , Ofosu Daniel Baah , Mack Cheryl , Majaesic Carina , van Manen Michael
Published: July 2023

Objectives

Children living with a tracheostomy have among the most complex medical care needs in Canada. The focus of this study was to gain a contemporary understanding of key aspects of these children’s medical journeys.

Methods

We conducted a qualitative constructivist grounded theory study using semi-structured focus groups with parents whose children are living in the community with a tracheostomy. Parents were recruited from the Stollery Children’s Hospital Tracheostomy Clinic, which serves a geographically wide and diverse population.

Results

Three focus groups were completed, including a total of 12 participants. Key themes leading up to tracheostomy related to contextual understanding, experiences of inclusion, and perceptions of proportionality. Parents discussed the preparedness for how a tracheostomy would affect their child, their own involvement in recovery, and the education needed for their child’s medical care. Navigating hospital units related to inconsistencies in care, accommodations of families’ needs, and confidence in care received. Finally, living in the community was the focus of much of the participants’ discussions including coping with system-related issues, limited homecare and medical support, cost of care, and connections with the broader community of parents of children with complex medical needs. All themes encircled the family’s deeply felt responsibility to care for their child.

Conclusions

From both patient- and family-centered care perspectives, there exist individual and systemic issues related to the care delivery for children with a tracheostomy. It is in particular in the community where there is a severe deficiency of support afforded to these children and their families.
Progress in Stem Cells-Based Replacement Therapy for Retinal Pigment Epithelium: In Vitro Differentiation to In Vivo Delivery
Authors: Gupta Santosh , Lytvynchuk Lyubomyr , Ardan Taras , Studenovska Hana , Sharma Ruchi , Faura Georgina , Eide Lars , Shanker Verma Rama , Znaor Ljubo , Erceg Slaven , Stieger Knut , Motlik Jan , Petrovski Goran , Bharti Kapil
Published: July 2023

Retinal pigment epithelium (RPE) is a critical cell monolayer forming the blood-retina-barrier (BRB) and a permeable bridge between the choriocapillaris and the retina. RPE is also crucial in maintaining photoreceptor function and for completing the visual cycle. Loss of the RPE is associated with the development of degenerative diseases like age-related macular degeneration (AMD). To treat diseases like AMD, pluripotent stem cell-derived RPE (pRPE) has been recently explored extensively as a regenerative module. pRPE like other ectodermal tissues requires specific lineage differentiation and long-term in vitro culturing for maturation. Therefore, understanding the differentiation process of RPE could be useful for stem cell-based RPE derivation. Developing pRPE-based transplants and delivering them into the subretinal space is another aspect that has garnered interest in the last decade. In this review, we discuss the basic strategies currently employed for stem cell-based RPE derivation, their delivery, and recent clinical studies related to pRPE transplantation in patients. We have also discussed a few limitations with in vitro RPE culture and potential solutions to overcome such problems which can be helpful in developing functional RPE tissue.
Systematics of the genusEuryoryzomysWeksleret al., 2006 (Rodentia: Cricetidae): integrative analysis reveals a new species from north-eastern Brazil
Authors: Percequillo Alexandre Reis , Weksler Marcelo
Published: July 2023

The genus Euryoryzomys encompasses six species found across Cis-Andean lowland and montane rainforests in South America. One of the most enigmatic forms of the genus is found in the Brejos de altitude of north-eastern Brazil, where enclaves of dense rainforest in mountain ranges sharply contrast with surrounding semi-arid Caatinga. Here we analyse morphological and molecular data, and demonstrate that these populations are members of a new species, which is described and contrasted with other Euryoryzomys. Phylogenetic analyses based on mitochondrial cytochrome b gene, coupled with morphometrics and comparative anatomy analyses, show that the new species differs from its sister-species, Euryoryzomys lamia from the Cerrado of Central Brazil, and from other forms of the genus, corroborating previous perspectives based on karyological data. The new species of the genus occurs in two distinct areas in the state of Ceará, Serra de Ibiapaba and Serra de Baturité, and one isolated range in Paraíba state. The recovered biogeographic pattern of Brejos de altitude—Cerrado sister-group relationship is novel among studied vertebrates, as most species from Brejos are more closely related to taxa from Amazon and Atlantic Forest. Further taxonomic efforts are necessary to uncover the total diversity within Euryoryzomys, especially for the nominal taxa E. emmonsae, E. macconnelli, and E. nitidus.
Pregnancy Outcomes With Donor Oocyte Embryos in Patients Diagnosed With Adenomyosis Using the Morphological Uterus Sonographic Assessment Criteria
Authors: Dason Ebernella Shirin , Maxim Madalina , Hartman Alexander , Li Qixuan , Kanji Salina , Li Tiantian , Ng Charis , Huszti Ella , Sobel Mara , Chan Crystal
Published: July 2023

(Abstracted from Fertil Steril 2023;119(3):484–489)

Adenomyosis is a benign gynecologic condition that causes endometrial glands and stroma to be found in the myometrium. Although the criterion-standard diagnosis of adenomyosis remains histology after hysterectomy, ultrasound diagnosis has allowed earlier detection, but no standard definition of imaging-based diagnosis exists.
A TGF-β–dominant chemoresistant phenotype of hepatoblastoma associated with aflatoxin exposure in children
Authors: Xiang Xiao , Hao Yijie , Cheng Cheng , Hu Huanjing , Chen Huadong , Tan Jiehui , Wang Yuanqi , Liu Xiaofei , Peng Bo , Liao Junbin , Wang Ji , Xie Yubin , liu Juncheng , Chen Shuling , Xu Lixia , Xie Wenxuan , Xue Ruidong , Kuang Ming , Xu Zhe , Jiang Hong , Peng Sui
Published: July 2023

Background and Aims:

Hepatoblastoma (HB) is the most common liver cancer in children, posing a serious threat to children’s health. Chemoresistance is the leading cause of mortality in patients with HB. A more explicit definition of the features of chemotherapy resistance in HB represents a fundamental urgent need.

Approach and Results:

We performed an integrative analysis including single-cell RNA sequencing, whole-exome sequencing, and bulk RNA sequencing in 180 HB samples, to reveal genomic features, transcriptomic profiles, and the immune microenvironment of HB. Multicolor immunohistochemistry staining and in vitro experiments were performed for validation. Here, we reported four HB transcriptional subtypes primarily defined by differential expression of transcription factors. Among them, the S2A subtype, characterized by strong expression of progenitor (MYCN, MIXL1) and mesenchymal transcription factors (TWIST1, TBX5), was defined as a new chemoresistant subtype. The S2A subtype showed increased TGF-β cancer-associated fibroblast and an immunosuppressive microenvironment induced by the upregulated TGF-β of HB. Interestingly, the S2A subtype enriched SBS24 signature and significantly higher serum aflatoxin B1-albumin (AFB1-ALB) level in comparison with other subtypes. Functional assays indicated that aflatoxin promotes HB to upregulate TGF-β. Furthermore, clinical prognostic analysis showed that serum AFB1-ALB is a potential indicator of HB chemoresistance and prognosis.

Conclusions:

Our studies offer new insights into the relationship between aflatoxin and HB chemoresistance and provide important implications for its diagnosis and treatment.
Context-dependent T-cell Receptor Gene Repertoire Profiles in Proliferations of T Large Granular Lymphocytes
Authors: Assmann Jorn L.J.C. , Vlachonikola Elisavet , Kolijn Pieter M. , Agathangelidis Andreas , Pechlivanis Nikolaos , Papalexandri Apostolia , Stamatopoulos Kostas , Chatzidimitriou Anastasia , Langerak Anton W.
Published: July 2023

T cell large granular lymphocyte (T-LGL) lymphoproliferations constitute a disease spectrum ranging from poly/oligo to monoclonal. Boundaries within this spectrum of proliferations are not well established. T-LGL lymphoproliferations co-occur with a wide variety of other diseases ranging from autoimmune disorders, solid tumors, hematological malignancies, post solid organ, and hematopoietic stem cell transplantation, and can therefore arise as a consequence of a wide variety of antigenic triggers. Persistence of a dominant malignant T-LGL clone is established through continuous STAT3 activation. Using next-generation sequencing, we profiled a cohort of 27 well-established patients with T-LGL lymphoproliferations, aiming to identify the subclonal architecture of the T-cell receptor beta (TRB) chain gene repertoire. Moreover, we searched for associations between TRB gene repertoire patterns and clinical manifestations, with the ultimate objective of discriminating between T-LGL lymphoproliferations developing in different clinical contexts and/or displaying distinct clinical presentation. Altogether, our data demonstrates that the TRB gene repertoire of patients with T-LGL lymphoproliferations is context-dependent, displaying distinct clonal architectures in different settings. Our results also highlight that there are monoclonal T-LGL cells with or without STAT3 mutations that cause symptoms such as neutropenia on one end of a spectrum and reactive oligoclonal T-LGL lymphoproliferations on the other. Longitudinal analysis revealed temporal clonal dynamics and showed that T-LGL cells might arise as an epiphenomenon when co-occurring with other malignancies, possibly reactive toward tumor antigens.
Venous Thromboembolism in Pediatric Inflammatory Bowel Disease: A Scoping Review
Authors: Gandhi Jermie , Mages Keith , Kucine Nicole , Chien Kimberley
Published: July 2023

Objectives:

In addition to gastrointestinal symptoms, pediatric inflammatory bowel disease (pIBD) may present with extra-intestinal manifestations including venous thromboembolism (VTE). Prevention and treatment guidelines for VTE in pediatric patients are needed. In this scoping review, we sought to detail the available data on the prevention and management of VTE in pIBD.

Methods:

Using PRISMA extension for Scoping Reviews (PRISMA-ScR), we identified, screened, graded quality of, and analyzed, literature on VTE in pediatric IBD, published between 1967 and 2023.

Results:

Data were extracted from 107 studies (including 216 patients). IBD patients with VTE had a median age of 14 years. Children with VTE more frequently had ulcerative colitis (70%, n = 216), developed their VTE within the first year of IBD diagnosis (52%, n = 97), had recent steroid use (62%, n = 50), and had central venous catheters (38%, n = 42). Cerebral venous sinus thrombus was the most common VTE type (34% of all VTE). Testing for thrombophilia conditions was rarely available but 65% (n = 23) of subjects tested had elevated Factor VIII activity. While most patients made a full recovery, 5% (n = 11) died secondary to their VTE.

Conclusions:

While randomized clinical trials assessing interventions to prevent and treat VTE in pIBD would be ideal, the feasibility of doing such studies is low. However, there has been an increase in interest in this topic and an increase in literature over the past decade. As such, a consensus statement from a multidisciplinary group of experts based on available literature and clinical experience would be valuable for practicing clinicians.
The Risks and Benefits of Monoclonal Antibody Therapy During Pregnancy and Postpartum: Maternal, Obstetric, and Neonatal Considerations
Authors: Wickenheisser Natalie E. , Craig Amanda M. , Kuller Jeffrey A. , Dotters-Katz Sarah K.
Published: July 2023

Importance

Autoimmune and rheumatologic conditions can lead to multiple adverse maternal, obstetric, and neonatal outcomes, especially if they flare during pregnancy. Although many medications to control these conditions exist, concerns regarding their safety often unnecessarily limit their use.

Objective

We aim to review the current evidence available describing the use of monoclonal antibody (mAb) therapeutics in pregnancy and postpartum and understand the impact of their use on the developing fetus and neonate.

Evidence Acquisition

Original research articles, review articles, case series and case reports, and pregnancy guidelines were reviewed.

Results

Multiple retrospective (including 1924 patients) and prospective studies (including 899 patients) of anti–tumor necrosis factor (TNF) agent use in pregnancy found no significant increase in rates of miscarriage, preterm birth, or congenital anomalies compared with controls. Most societies, including American College of Obstetricians and Gynecologists and Society for Maternal-Fetal Medicine, recommend initiation or continuation of TNF-α inhibitors during pregnancy for patients with autoimmune diseases. An increased risk of mild infections in newborns has been reported, although infections requiring hospitalizations are rare. Data suggest that breastfeeding while taking anti-TNF agents is safe for neonates. Less data exist for the use of other mAbs including anticytokine, anti-integrin, and anti–B-cell agents during pregnancy and postpartum.

Conclusions and Relevance

Current evidence suggests that the use of mAbs, particularly anti-TNF agents, is safe in pregnancy and postpartum, without significant adverse effects on the pregnant patient or infant. The benefits of ongoing disease control in pregnant patients result in favorable maternal and neonatal outcomes.

Target Audience

Obstetricians and gynecologists, family physicians.

Learning Objectives

After participating in this activity, the provider should be better able to explain the benefits of using mAb therapies or biologics in pregnant patients; discuss the known and theoretical risks of using mAb therapies during pregnancy on neonates; and describe the risks and benefits of continuing mAb therapy while breastfeeding.
Prescription Opioid Use for Acute Pain and Persistent Opioid Use After Gynecologic Surgery: A Systematic Review
Authors: Matteson Kristen A. , Schimpf Megan O. , Jeppson Peter C. , Thompson Jennifer C. , Gala Rajiv B. , Balgobin Sunil , Gupta Ankita , Hobson Deslyn , Olivera Cedric , Singh Ruchira , White Amanda B. , Balk Ethan M. , Meriwether Kate V. ,   for the Society of Gynecologic Surgeons Systematic Review Group
Published: July 2023

(Abstracted from Obstet Gynecol 2023;141:681–696)

Although opioid analgesics can be an effective pain control method in the acute postoperative period, their use comes with risks such as opioid misuse, persistent use, or opioid use disorders. As most postsurgical patients use less than half of their prescribed opioids (and rarely dispose of unused medication), millions of legitimately prescribed opioid tablets are available for diversion and misuse annually.
Endoscopic Surveillance for Colorectal Cancer in Pediatric Ulcerative Colitis: A Survey Among Dutch Pediatric Gastroenterologists
Authors: Jagt Jasmijn Z. , van Schie Daniëlle A. , Benninga Marc A. , van Rheenen Patrick F. , de Boer Nanne K. H. , de Meij Tim G. J. ,   on behalf of the Kids with Crohn’s, Colitis (KiCC) Working Group for Collaborative Paediatric IBD Research in the Netherlands
Published: July 2023

Objectives:

This study aimed to evaluate the current clinical practice of Dutch pediatric gastroenterologists regarding the surveillance for colorectal dysplasia and cancer in pediatric ulcerative colitis (UC), including adherence to guidelines, the initiation and interval of surveillance and applied endoscopy techniques.

Methods:

A clinical vignette-based survey was distributed among all 47 pediatric gastroenterologists who are registered and working in the Netherlands.

Results:

Thirty-three pediatric gastroenterologists treating children with UC, completed the questionnaire (response rate 70%). Of these respondents, 23 (70%) do conduct endoscopic surveillance in their UC patients. Adherence to any of the available guidelines was reported by 82% of respondents. Twenty-four of 31 respondents (77%) indicated the need for development of a new guideline. Profound variation was witnessed concerning the initiation and interval of surveillance, and risk factors taken into consideration, such as disease extent and concomitant diagnosis of primary sclerosing cholangitis (PSC). The available national and European guidelines recommend the use of chromoendoscopy in the performance of surveillance. This technique was conducted by 8% of respondents, whereas 50% conducted conventional endoscopy with random biopsies.

Conclusions:

The heterogeneity in surveillance practices underlines the need for consistency among the guidelines, explicitly stated by 77% of the respondents. For this, future research on surveillance in pediatric UC is warranted, focusing on the risk of UC-associated colorectal cancer related to risk factors and optimal endoscopy techniques.
Pessary Management Approach Affects Likelihood of Surgery
Authors: Chen Yufan Brandon , Lowe Christian , Wozniak Amy , Pham Thythy T. , Fitzgerald Colleen M. , Mueller Elizabeth R. , Acevedo-Alvarez Marian
Published: July 2023

Importance

It is unknown whether the pessary management type influences the need for surgery.

Objective

The aim of this study was to evaluate the rate of surgical treatment for pelvic organ prolapse or stress urinary incontinence with the type of pessary management (self-management or office management).

Study Design

We conducted a retrospective cohort study that included first-time pessary users treated at a tertiary urogynecologic clinic from 2012 to 2014 for pelvic organ prolapse, stress urinary incontinence, or both. For the primary outcome, we explored the relationship between pessary management type and the likelihood of surgery using multivariable Cox proportional hazards models. Secondary outcomes assessed relationships between patient factors (eg, demographics and clinical attributes) and pessary management type using multivariable logistics regression models.

Results

There were 218 patients included in our analysis. Of all pessary users, 59 (27.1%) required office management and 159 (72.9%) participated in self-management. Surgery was performed in 22 (35.1%) office-managed patients and 33 (19.3%) self-managed patients. Women who self-managed their pessaries were significantly less likely to undergo surgery than those who received office management (multivariable hazards ratios, 0.416; P = 0.005). In the multivariable logistic regression model for pessary management type, increasing age (odds ratio [OR], 1.098; P ≤ 0.0001), increasing body mass index (OR, 1.078; P < 0.05), and increasing genital hiatus (OR, 1.547; P < 0.05) were associated with increased odds of pessary office management compared with self-management.

Conclusions

In a urogynecology clinic setting, pessary self-management is associated with lower rates of surgical treatment compared with office management. Factors associated with office management include increased age, body mass index, and large genital hiatus.
Outcomes of Pessary Use at 1 Year in Women Treated for Pelvic Organ Prolapse in a Large Multicenter Registry
Authors: Yurteri-Kaplan Ladin A. , Meyn Leslie , Moalli Pam A. , Bradley Catherine S. , Foster Raymond T. , Andy Uduak U. , Guaderrama Noelani , Gutman Robert E. , Anger Jennifer T. , Hull Amy , Propst Katie , Shippey Stuart S. , Brown Heidi W.
Published: July 2023

Importance

There is a lack of high-quality long-term follow-up regarding pessary treatment. Most studies are case series or retrospective with a small sample size and short-term follow-up.

Objectives

This study aimed to evaluate differences in women who continue versus discontinue pessary use and the effectiveness, quality of life, and safety associated with pessary management at 1 year.

Study Design

This study analyzed a multicenter national registry following women for 3 years with vaginal prolapse treated with a pessary or surgery. The primary outcome of this analysis was to compare the difference in characteristics among those who continue versus discontinue pessary use at 12 months.

Results

Among 1,153 participants enrolled, 376 (32.6%) opted for a pessary, and 296 (78.7%) were successfully fitted. Data were available for 240 participants (81%). At 1 year, 62% (n = 148) were still using pessaries, and 38% (n = 92) had stopped with 25% opting for surgery. Most commonly reported de novo adverse effects were urinary leakage (16%), feeling or seeing a bulge (12%), and vaginal discharge (11%). There was no difference in baseline characteristics among women who continued versus discontinued pessary use. At 12 months, subjective symptoms were similar between groups, with similar change in symptoms from baseline on most validated instruments. Those who continued to use a pessary reported worse urinary symptoms due to de novo urinary leakage (P = 0.01).

Conclusions

At 1 year, most women successfully fitted with a pessary continued pessary use. Although there was a significant improvement in condition-specific quality of life and low rates of complications, approximately 40% of women discontinued pessary use by 12 months. We were unable to identify any baseline characteristics associated with pessary discontinuation.
Unusually isolated Staphylococcus arlettae in intra-oral sutures- Case series
Authors: KHERDEKAR RADHIKA SUNIL , DIXIT ASHUTOSH , KOTHARI ASHISH , PANDEY KAMAL PRASAD , ADVANI HOSHANG , GAURAV AMIT , OMAR BALRAM JI
Published: July 2023

Introduction: The human oral cavity comprises various niches such as teeth, gingiva, tongue, soft and hard palate, and various dental prostheses, all inhabited by different bacterial species. Although more than 600 taxa belong to the oral cavity, identifying Staphylococcus arlettae, an incompletely understood bacterium, has been rare.
Methods: Three patients who underwent periodontal flap surgeries were reported with the incidental finding of S. arlettae associated with the intra-oral sutures placed. Environmental sampling was performed, to establish the exact source of this bacterium.
Results: Staphylococcus arlettae was isolated in three patients’ intra-oral sutures. All environmental samples were negative for the presence of the bacterium.
Conclusion: To this date, no studies have identified such an occurrence of Staphylococcus arlettae with intra-oral sutures. Its identification in association with foreign materials, such as sutures, can be considered a potential for surgical site infections and requires further investigation.
A case report of disseminated Streptococcus pneumoniae infection complicated by infective endocarditis, septic arthritis and epidural abscess in an immunocompetent patient
Authors: Dean Kimberley Rose , Koirala Archana , Samarasekara Harsha
Published: July 2023

Streptococcus pneumoniae

is a highly virulent, vaccine-preventable pathogen which can cause disease on a spectrum from benign to fatal. Apart from pneumonia, it commonly causes septicaemia and meningitis. This case report describes an unusual range of complications in a 53-year-old Caucasian female presenting to a regional hospital, without any risk known factors for severe disease (such as extremes of age, immunodeficiency or co-morbidities). Progressing from an episode of otitis media, her condition rapidly progressed to mastoid sinusitis, septic arthritis, infective endocarditis, epidural abscesses and multiple subcutaneous abscesses. Following quick identification of

S. pneumoniae

from a positive blood culture, the patient was treated with high-dose benzylpenicillin and ceftriaxone and aggressive source control by surgery, enabling a good clinical recovery.
MosaiCatcher v2: a single-cell structural variations detection and analysis reference framework based on Strand-seq
Authors: Weber Thomas , Cosenza Marco Raffaele , Korbel Jan
Published: July 2023

Single-cell DNA template strand sequencing (Strand-seq) allows a range of various genomic analysis including chromosome length haplotype phasing and structural variation (SV) calling in individual cells. Here, we present MosaiCatcher v2, a standardised workflow and reference framework for single-cell SV detection using Strand-seq. This framework introduces a range of functionalities, including: an automated upstream Quality Control (QC) and assembly sub-workflow that relies on multiple genome assemblies and incorporates a multistep normalisation module, integration of the scNOVA SV functional characterization and of the ArbiGent SV genotyping modules, platform portability, as well as a user-friendly and shareable web report. These new features of MosaiCatcher v2 enables reproducible computational processing of Strand-seq data, which are increasingly used in human genetics and single cell genomics, towards production environments.

Availability and Implementation

Mosaicatcher v2 is a standardised workflow, implemented using the Snakemake workflow management system. The pipeline is available on GitHub:https://github.com/friendsofstrandseq/mosaicatcher-pipeline/and on the snakemake-workflow-catalog:

https://snakemake.github.io/snakemake-workflow-catalog/?usage=friendsofstrandseq/mosaicatcher-pipeline.

Contact

jan.korbel@embl.de

Supplementary information

Supplementary data are available at Bioinformatics online.
Ischaemic Preconditioning attenuates Chronic Renal Damage following Ischaemia Reperfusion Injury
Authors: Brown Charlotte Victoria Maynard , Pino-Chavez Gilda , Zaidi Aeliya , Grigorieva Irina , Woods Emma , Steadman Robert , Chavez Rafael , Meran Soma , Khalid Usman
Published: July 2023

Acute Kidney Injury (AKI) is a common cause of Chronic Kidney Disease (CKD). The leading cause of AKI worldwide is Ischaemia Reperfusion Injury (IRI), seen most commonly in the clinical setting as a result of sepsis-driven hypotension. We are increasingly recognising, however, that AKI and CKD are one closely associated continuum of disease, rather than distinct entities. Ischaemic Preconditioning (IPC) is a strategy aimed at reducing the deleterious effects of IRI. This study demonstrates an efficacious model of kidney IRI, and the protective influence of IPC in attenuating renal injury/fibrosis.

A rat model of bilateral kidney IRI was used: Male Lewis rats (n=84) were assigned to IRI, sham or IPC. In IRI, renal pedicles were clamped for 45 minutes. IPC groups underwent pulsatile IPC prior to IRI. Kidneys were retrieved at 24-hours, 48-hours, 7-days, 14-days and 28-days, and assessed histologically.

IRI led to marked histological damage and renal fibrosis development by 28 days. Histological injury scores and degree of fibrosis were significantly increased following IRI and attenuated with IPC. IPC resulted in a 66% reduction in renal fibrosis at 28 days (p<0.001). IRI also led to a significant increase in serum creatinine acutely, which was attenuated by IPC (p<0.0001). Interestingly at 14-days, there was limited histological damage and differentiation between IRI and IPC kidneys was difficult.

IPC can protect from both acute and chronic kidney damage. 14-days post IRI represents a transitional phase, which maybe a timepoint for commitment to either fibrosis or recovery, and hence offers potential for therapeutic intervention.
Extended lifespan in femaleDrosophila melanogasterthrough late-life caloric restriction
Authors: Li Michael , Macro Jacob , Huggins Billy J. , Meadows Kali , Mishra Dushyant , Martin Dominique , Rogina Blanka
Published: July 2023

Calorie restriction has many beneficial effects on healthspan and lifespan in a variety of species. However, how late in life application of caloric restriction can extend fly life is not clear. Here we show that late-life calorie restriction increases lifespan in femaleDrosophila melanogasteraged on a high calorie diet. This shift results in rapid decrease in mortality rate and extends fly lifespan. In contrast, shifting female flies from a low to a high calorie diet leads to a rapid increase in mortality and shorter lifespan. These changes are mediated by immediate metabolic and physiological adaptations. One of such adaptation is rapid adjustment in egg production, with flies directing excess energy towards egg production when shifted to a high diet, or away from reproduction in females shifted to low caloric diet. However, lifelong female fecundity reveals no associated fitness cost due to CR when flies are shifted to a high calorie diet. In view of high conservation of the beneficial effects of CR on physiology and lifespan in a wide variety of organisms, including humans, our findings could provide valuable insight into CR applications that could provide health benefits later in life.
Precise Nanopore Signal Modeling Improves Unsupervised Single-Molecule Methylation Detection
Authors: Boža Vladimír , Batmendijn Eduard , Perešíni Peter , Hodorová Viktória , Lichancová Hana , Rabatin Rastislav , Brejová Broňa , Nosek Jozef , Vinař Tomáš
Published: July 2023

Base calling in nanopore sequencing is a difficult and computationally intensive problem, typically resulting in high error rates. In many applications of nanopore sequencing, analysis of raw signal is a viable alternative. Dynamic time warping (DTW) is an important building block for raw signal analysis. In this paper, we propose several improvements to DTW class of algorithms to better account for specifics of nanopore signal modeling. We have implemented these improvements in a new signal-to-reference alignment tool Nadavca. We demonstrate that Nadavca alignments improve unsupervised methylation detection over Tombo. We also demonstrate that by providing additional information about the discriminative power of positions in the signal, an otherwise unsupervised method can approach the accuracy of supervised models.

Availability and implementation

Nadavca is available under MIT license athttps://github.com/fmfi-compbio/nadavca. Nanopore sequencing data sets are available from ENA bioproject PRJEB64246.Jaminaea angkorensisreference genome assembly is available from Zenodohttps://doi.org/10.5281/zenodo.8145315.
Explanation of saltatory conduction in myelinated axons and of micro-saltatory conduction in C fibers of pain sensation by a wave-type ion plasmonic mechanism of stimulus kinetics
Authors: Jacak J. E. , Jacak W. A.
Published: July 2023

Ion plasmon-polariton model of stimulus in myelinated axons and in C fibers of pain sensation is developed. This solves a long standing problem in neuroscience of by 2 − 3 orders of magnitude discrepancy between the observed fast speed of the saltatory conduction in myelinated axons or in C fibers with the upper limit of diffusive ion current velocity in these axons. The latter, described in the framework of so-called cable model, is too low in axons because of poor conductivity of neuron inner cytosol. The compliance with observations has been achieved upon plasmonic model of ionic local oscillations synchronized in periodically corrugated axons and propagating with high speed in the form of wave-type plasmon-polariton without any net diffusion current, thus not limited by resistivity. The new model of stimulus in myelinated axons reveals the different controlling role of myelin than previously thought from cable model. The control mechanism in non-myelinated C fibers is also proposed in agreement with observations. Recognition of plasmon model of neural signaling may be important for identifying a new targets for the future treatment at demyelination diseases and for fighting pain.
tfboot: Bootstrapping and statistical analysis for transcription factor binding site-disrupting variants in gene sets
Authors: Turner Stephen D. , Morrill Kathleen , Gedman Gregory , Titus Alexander J.
Published: July 2023

Motivation

Genetic variants in noncoding regions can drive changes in phenotype disrupting transcription factor binding site (TFBS) motifs. Other tools including motifbreakR have been developed to assess the impact of TFBS-disrupting variants. Here we introduce the tfboot package for statistically evaluating the TFBS disruption across asetof variants in upstream promoter regions.

Results

The tfboot package builds on motifbreakR, plyranges, and GenomicRanges to provide methods for bootstrapping TFBS disruption to statistically quantify the impact across gene sets of interest compared to an empirical null distribution. We demonstrate the analysis here on variants in the elephant genome. The tfboot package readily integrates with Bioconductor and tidyverse-based workflows.

Availability

The tfboot package is implemented as an R package and is released under the MIT license athttps://github.com/colossal-compsci/tfboot.
Prospects and pitfalls of an intrusive model for the Châtelperronian stone tool industry during the Middle to Upper Palaeolithic transition in France and northern Spain
Authors: Djakovic Igor , Roussel Morgan , Soressi Marie
Published: July 2023

The Middle to Upper Palaeolithic transition in France and northern Spain reflects the transition from Neandertals toHomo sapiensand the emergence of novel cultural entities and standardised laminar technologies between ~50 and 40 thousand years ago. The Châtelperronian stone tool industry sits at the centre of this period, and is commonly considered as representing a geographically isolated archaeological entity produced by late Neandertals. However, debate as to the makers and origin of this industry has long persisted. Fuel has recently been thrown onto this discussion through the formulation of a hypothesis in which the Châtelperronian directly originates from the Northern Early Ahmarian industry of the Levant. This model proposes that the Châtelperronian is in fact indicative of a direct migration of a population ofHomo sapiensfrom the Levant to France around 44-40 thousand years ago – potentially via the crossing (or series of crossings) of the Mediterranean Sea. Such a scenario would have significant implications for how we interpret this key portion of recent human evolutionary history. In this paper, we highlight some of the prospects and pitfalls of an intrusive origin model for the emergence of the Châtelperronian industry in western Europe - taking into account technological, chronological, geographic, and stratigraphic perspectives. To frame this discussion, we review the state of understanding on the Châtelperronian and provide a detailed, synthetic review of Châtelperronian lithic technology. Our review reinforces the distinctive and fully ‘Upper Palaeolithic’ character of this industry, and we subsequently suggest a few avenues of research which, in our opinion, may help shed progressively clearer light on the demographic and cultural processes operating during the Middle to Upper Palaeolithic transition in western Europe.