bluuebunny/crossref_metadata_2025_split huggingface dataset:
Drivers of infection with Toxoplasma gondii genotype type II in Eurasian red squirrels (Sciurus vulgaris)
Authors: Wijburg Sara R. , Montizaan Margriet G. E. , Kik Marja J. L. , Joeres Maike , Cardron Garance , Luttermann Christine , Maas Miriam , Maksimov Pavlo , Opsteegh Marieke , Schares Gereon 
Published: January 2024

Abstract
Background
In September 2014, there was sudden upsurge in the number of Eurasian red squirrels (Sciurus vulgaris) found dead in the Netherlands. High infection levels with the parasite Toxoplasma gondii were demonstrated, but it was unclear what had caused this increase in cases of fatal toxoplasmosis. In the present study, we aimed to gain more knowledge on the pathology and prevalence of T. gondii infections in Eurasian red squirrels in the Netherlands, on the T. gondii genotypes present, and on the determinants of the spatiotemporal variability in these T. gondii infections. The presence of the closely related parasite Hammondia hammondi was also determined.

Methods
Eurasian red squirrels that were found dead in the wild or that had died in wildlife rescue centres in the Netherlands over a period of seven years (2014–2020) were examined. Quantitative real-time polymerase chain reaction was conducted to analyse tissue samples for the presence of T. gondii and H. hammondi DNA. Toxoplasma gondii-positive samples were subjected to microsatellite typing and cluster analysis. A mixed logistic regression was used to identify climatic and other environmental predictors of T. gondii infection in the squirrels.

Results
A total of 178 squirrels were examined (49/178 T. gondii positive, 5/178 H. hammondi positive). Inflammation of multiple organs was the cause of death in 29 squirrels, of which 24 were also T. gondii polymerase chain reaction positive. Toxoplasma gondii infection was positively associated with pneumonia and hepatitis. Microsatellite typing revealed only T. gondii type II alleles. Toxoplasma gondii infection rates showed a positive correlation with the number of days of heavy rainfall in the previous 12 months. Conversely, they showed a negative association with the number of hot days within the 2-week period preceding the sampling date, as well as with the percentage of deciduous forest cover at the sampling site.

Conclusions
Toxoplasma gondii infection in the squirrels appeared to pose a significant risk of acute mortality. The T. gondii genotype detected in this study is commonly found across Europe. The reasons for the unusually high infection rates and severe symptoms of these squirrels from the Netherlands remain unclear. The prevalence of T. gondii in the deceased squirrels was linked to specific environmental factors. However, whether the increase in the number of dead squirrels indicated a higher environmental contamination with T. gondii oocysts has yet to be established.

Graphical Abstract
Assessing the microbiota of the snail intermediate host of trematodes, Galba truncatula
Authors: McCann Peter , McFarland Christopher , Megaw Julianne , Siu-Ting Karen , Cantacessi Cinzia , Rinaldi Gabriel , Gobert Geoffrey N. 
Published: January 2024

Abstract
Background
The microbiome is known to play key roles in health and disease, including host susceptibility to parasite infections. The freshwater snail Galba truncatula is the intermediate host for many trematode species, including the liver and rumen flukes Fasciola hepatica and Calicophoron daubneyi, respectively. The snail-parasite system has previously been investigated. However, the specific interaction between the snail-associated microbiota and intra-snail developmental stages of trematodes has yet to be explored.

Methods
Galba truncatula snails were collected from farms in Northern Ireland and trematode infection was diagnosed using PCR. High-throughput sequencing analysis of the bacterial 16S ribosomal DNA V3-V4 hypervariable regions was subsequently applied to characterise the microbiota of both uninfected and infected snails.

Results
We first showed that the snail harboured microbiota that was distinct for its environment. The microbiota of infected snails was found to differ significantly from that of uninfected snails. In particular, the bacterial genera Mycoplasma and Methylotenera were significantly more abundant in infected snails, while genera Sphingomonas and Nocardioides were predominantly associated with uninfected snails.

Conclusion
These findings pave the way to future studies on the functional roles of bacteria in host-parasite relationships.

Graphical Abstract
An insidious rectus abdominis muscle injury in an elite volleyball player: a case report
Authors: Giarda Federico , Contro Diego , Fasano Maurizio , Poli Mirko , Giacchino Maurizio 
Published: January 2024

Abstract
Background
Structural muscle injuries are characterized by acute and localized onset of pain. Abdominal muscle injuries are an insidious pathology in overhead athletes. However, only a few cases are reported in literature related to volleyball players, where clinical presentation may not have reflected the severity of the lesion.

Case presentation
An elite volleyball player, a 21-year-old Caucasian female, reported the onset of mild abdominal muscular pain, confirmed on clinical evaluation findings and self-reported symptoms. Abdominal muscle ultrasound was performed following 2 weeks of continuing symptoms. This evidenced a more serious structural muscle injury of the rectus abdominis (type 3b). Having this correct diagnosis allowed a personalized rehabilitation program to be instituted to enable a safe return to play.

Conclusion
In presence of persistent abdominal muscle pain, even if mild, the possibility of a structural muscle injury must be considered. Clinical evaluation must be complemented by an instrumental evaluation including an ultrasound by an experienced operator for correct diagnosis and the setting of functional recovery related to biological healing.
Deep learning-based algorithm for the detection of idiopathic full thickness macular holes in spectral domain optical coherence tomography
Authors: Valentim Carolina C. S. , Wu Anna K. , Yu Sophia , Manivannan Niranchana , Zhang Qinqin , Cao Jessica , Song Weilin , Wang Victoria , Kang Hannah , Kalur Aneesha , Iyer Amogh I. , Conti Thais , Singh Rishi P. , Talcott Katherine E. 
Published: January 2024

Abstract
Background
Automated identification of spectral domain optical coherence tomography (SD-OCT) features can improve retina clinic workflow efficiency as they are able to detect pathologic findings. The purpose of this study was to test a deep learning (DL)-based algorithm for the identification of Idiopathic Full Thickness Macular Hole (IFTMH) features and stages of severity in SD-OCT B-scans.

Methods
In this cross-sectional study, subjects solely diagnosed with either IFTMH or Posterior Vitreous Detachment (PVD) were identified excluding secondary causes of macular holes, any concurrent maculopathies, or incomplete records. SD-OCT scans (512 × 128) from all subjects were acquired with CIRRUS™ HD-OCT (ZEISS, Dublin, CA) and reviewed for quality. In order to establish a ground truth classification, each SD-OCT B-scan was labeled by two trained graders and adjudicated by a retina specialist when applicable. Two test sets were built based on different gold-standard classification methods. The sensitivity, specificity and accuracy of the algorithm to identify IFTMH features in SD-OCT B-scans were determined. Spearman’s correlation was run to examine if the algorithm’s probability score was associated with the severity stages of IFTMH.

Results
Six hundred and one SD-OCT cube scans from 601 subjects (299 with IFTMH and 302 with PVD) were used. A total of 76,928 individual SD-OCT B-scans were labeled gradable by the algorithm and yielded an accuracy of 88.5% (test set 1, 33,024 B-scans) and 91.4% (test set 2, 43,904 B-scans) in identifying SD-OCT features of IFTMHs. A Spearman’s correlation coefficient of 0.15 was achieved between the algorithm’s probability score and the stages of the 299 (47 [15.7%] stage 2, 56 [18.7%] stage 3 and 196 [65.6%] stage 4) IFTMHs cubes studied.

Conclusions
The DL-based algorithm was able to accurately detect IFTMHs features on individual SD-OCT B-scans in both test sets. However, there was a low correlation between the algorithm’s probability score and IFTMH severity stages. The algorithm may serve as a clinical decision support tool that assists with the identification of IFTMHs. Further training is necessary for the algorithm to identify stages of IFTMHs.
Electronic correlation and s-wave pairing effects in hole-doped LiNbO2: A DFT+DMFT study
Authors: Craco L. 
Published: January 2024

Abstract
We compute the electronic many-particle properties of the normal and s-wave superconducting state of hole-doped lithium niobite (LiNbO2), taking into account local dynamical correlations by means of density functional plus dynamical mean-field theory (DFT+DMFT). Our results for the one-band Hubbard model yield a consistent picture for the electronic structure reconstruction of Li
x
NbO2 and point at the importance of single-band electron correlations for understanding the emergent collective superfluid spectra as well as the hidden nature of the Fermi liquid electronic state that might host a s-wave superconducting phase at low teperatures.
Orbital selectivity in Sn adatom adlayer on a Si(111) surface
Authors: Craco Luis , Carara Sabrina S. 
Published: January 2024

Abstract
Unconventional quantum many-particle phenomenon naturally emerges when approaching the Mott-Hubbard insulating state. Finding insulator-metal transition in correlated adatoms in semiconductor surfaces provides an ideal material platform to design electronic states which may host superconductivity in two-dimensional electron systems. To uncover the microscopics underlying by multi-orbital interactions, we perform density functional plus dynamical mean-field theory calculations for the all-electron

Hubbard model, unraveling a Mott assisted Kondo insulating state in the atomic Sn layer deposited onto a Si(111) surface, also referred to as α-Sn. We propose that α-Sn is an ideal testing ground to explore hidden orbital selectivity and pseudogap behavior all arising from Mottness and discuss the relevance of our results for pure and hole-doped α-Sn in the context of spectroscopy and tunnelling experiments of adatom lattices.
Autosomal Dominant Osteopetrosis (ADO) Caused by a Missense Variant in the TCIRG1 Gene
Authors: Jodeh Wade , Katz Amy J , Hart Marian , Warden Stuart J , Niziolek Paul , Alam Imranul , Ing Steven , Polgreen Lynda E , Imel Erik A , Econs Michael J 
Published: January 2024

Abstract

Context
Autosomal dominant osteopetrosis (ADO) is a rare genetic disorder resulting from impaired osteoclastic bone resorption. Clinical manifestations frequently include fractures, osteonecrosis (particularly of the jaw or maxilla), osteomyelitis, blindness, and/or bone marrow failure. ADO usually results from heterozygous missense variants in the Chloride Channel 7 gene (CLCN7) that cause disease by a dominant negative mechanism. Variants in the T-cell immune regulator 1 gene (TCIRG1) are commonly identified in autosomal recessive osteopetrosis but have only been reported in 1 patient with ADO.

Case Description
Here, we report 3 family members with a single heterozygous missense variant (p.Gly579Arg) in TCIRG1 who have a phenotype consistent with ADO. Three of 5 protein prediction programs suggest this variant likely inhibits the function of TCIRG1.

Conclusion
This is the first description of adult presentation of ADO caused by a TCIRG1 variant. Similar to families with ADO from CLCN7 mutations, this variant in TCIRG1 results in marked phenotype variability, with 2 subjects having severe disease and the third having very mild disease. This family report implicates TCIRG1 missense mutations as a cause of ADO and demonstrates that the marked phenotypic variability in ADO may extend to disease caused by TCIRG1 missense mutations.
How Parental Incarceration Shapes the Timing and Structure of Fertility for Children of Incarcerated Parents
Authors: McCauley Erin J. 
Published: January 2024

AbstractThe timing and structure of fertility have important implications for individuals and society. Families play a critical role in fertility; however, little is known about how parental incarceration shapes fertility despite it being a common experience in the life course of disadvantaged children. This study examines the consequences of parental incarceration for children's fertility using the National Longitudinal Survey of Youth 1997. I employ multiple-decrement life tables and survival analyses to estimate the relationship between parental incarceration and fertility. Individuals who experience parental incarceration have different timing of fertility, with earlier first births and a quicker pace of subsequent births, as well as more nonmarital fertility, compared with those who do not experience parental incarceration. This analysis finds consistent evidence that parental incarceration is associated with the timing and structure of fertility and suggests that a parent's incarceration carries consequences over the life course of children. This study advances our understanding of how mass incarceration shapes American families, illustrates how the broader consequences of mass incarceration contribute to social inequality, and provides evidence that the enduring implications of incarceration span multiple generations.
Responses to Sexual and Gender Identity Measures in Population-Level Data by Birth Cohort: A Research Note
Authors: Julian Christopher A. , Manning Wendy D. , Westrick-Payne Krista K. 
Published: January 2024

Abstract
The measurement of sexual and gender identity in the United States has been evolving to generate more precise demographic estimates of the population and a better understanding of health and well-being. Younger cohorts of sexual- and gender-diverse adults are endorsing identities outside of the lesbian, gay, bisexual, and transgender (LGBT) labels. Current population-level surveys often include a category such as “something else” without providing further details, and doing so inadequately captures these diverse identities. In this research note, our analysis of the most recent federal data source to incorporate sexual and gender identity measures—the Household Pulse Survey—reveals that younger birth cohorts are more likely to select “something else” for their sexual identity and “none of these” for their gender identity. The observed sexual and gender identity response patterns across birth cohorts underscore the importance of developing and applying new strategies to directly measure sexual- and gender-diverse adults who identify with identities outside of those explicitly captured on surveys. The integration of sexual and gender identity measures in population-level surveys carries broader implications for civil rights and for addressing health inequities and therefore must be responsive to cohort differences in identification.
Two-Stage Anatomic Myocutaneous Flap Dissection in Cranioplasty: Technical Nuances and Single-Surgeon Experience
Authors: Sorek Sahar , Miller Aaron , Griepp Daniel , Mathew Vincy , Moawad Stephanie , Rahme Ralph 
Published: January 2024

BACKGROUND AND OBJECTIVES:
Temporalis muscle management remains one of the most challenging aspects of cranioplasty, which accounts for considerable rates of dissection-related complications. Since 2019, the senior author has developed and consistently used a methodical, two-stage anatomic dissection technique to separate the scalp and temporalis muscle from the underlying brain. This technique is believed to facilitate dissection and minimize the risk of brain injury, while optimizing cosmetic outcomes.

METHODS:
All patients who underwent cranioplasty between January 2019 and February 2023 were identified from a prospectively maintained database. Charts were retrospectively reviewed. Demographic, clinical, and procedural data were extracted and analyzed.

RESULTS:
Twenty-nine patients, 20 men and 9 women with a median age of 37 years (range 17-72), were identified. Indications for craniectomy were traumatic brain injury in 18 (62.1%), hemorrhagic stroke in five (17.2%), ischemic stroke in four (13.8%), and aneurysmal subarachnoid hemorrhage in two (6.9%). Median precranioplasty modified Rankin Scale and Glasgow Coma Scale scores were 5 (range in series: 0-5) and 14 (range in series: 3-15), respectively. The median time to cranioplasty was 131 days (32-1717). Cranioplasty was technically successful in all patients, with a median operative time of 106 minutes (62-182). There were no intraoperative complications. Postoperative complications occurred in three patients (10.3%): hemorrhagic brain contusion (n = 1), meningitis (n = 1), and seizure (n = 1). Of those, one patient (3.4%) died 2 weeks after surgery from suspected pulmonary embolism. After a median follow-up of 4 months (1-44), all 28 survivors have either remained clinically stable or exhibited neurological improvement. Cosmetic results were good or excellent in 27 (96.4%) and fair in one (3.6%).

CONCLUSION:
Two-stage anatomic dissection of the scalp and temporalis muscle during cranioplasty can maximize surgical efficiency and result in excellent outcomes. Cranioplasty should be considered a low-risk, low-complexity neurosurgical procedure. Safe and efficient management of the temporalis muscle is key.
Establishing mouse and human oral esophageal organoids to investigate the tumor immune response
Authors: Jiang Yuan , Zhao Hua , Kong Shuai , Zhou Dan , Dong Jinxiu , Cheng Yulan , Zhang Shuo , Wang Fei , Kalra Andrew , Yang Nina , Wei Dan-Dan , Chen Jian , Zhang Yuan-Wei , Lin De-Chen , Meltzer Stephen J. , Jiang Yan-Yi 
Published: January 2024

ABSTRACT
Organoid culture systems are very powerful models that recapitulate in vivo organ development and disease pathogenesis, offering great promise in basic research, drug screening and precision medicine. However, the application of organoids derived from patients with cancer to immunotherapeutic research is a relatively untapped area. Esophageal cancer is one of the most lethal malignancies worldwide, including two major pathological subtypes: esophageal squamous cell carcinoma (ESCC) and esophageal adenocarcinoma. ESCC shares many biological and genomic features with oral squamous cell cancers. Herein, we provide a versatile protocol for the establishment and maintenance of oral and esophageal organoid cultures derived from both murine and human samples. We describe culture conditions for organoids derived from normal tongue, esophagus and gastroesophageal junction, esophageal cancer and Barrett's esophagus. In addition, we establish an ex vivo model by co-culturing patient tumor-derived organoids and autologous CD8+ T lymphocytes to assess CD8+ T cell-mediated tumor killing. Our protocol can also be modified for organoid establishment from other squamous epithelia and carcinomas. The co-culture model can serve as a template for studies of other tumor-immune cell interactions and the efficacy of immune checkpoint blockade therapy.
Ultracompact and ultrabroadband arbitrary ratio power splitter using subwavelength gratings
Authors: Lu Mengjia , Guo Zhenzhao , Deng Chunyu , Hu Xuefang , Chen Mengmeng 
Published: January 2024

An ultracompact and ultrabroadband arbitrary ratio power splitter based on adiabatically tapered silicon waveguides, with subwavelength gratings in the coupling region, is proposed and demonstrated experimentally. Various power splitting ratios (PSRs) can be implemented by flexibly manipulating the gap of two adjacent tapered waveguides. The wavelength dependence is greatly reduced by introducing subwavelength gratings. Simulation results show that our proposed device has a 400 nm (1300 nm–1700 nm) bandwidth with an insertion loss <0.5dB for PSRs of 50:50, 60:40, 70:30, 80:20, and 90:10, and the corresponding total device length is only 2.9 µm. The experimental results indicate that the insertion loss is lower than 0.82 dB over a wide bandwidth of 80 nm, and there is a PSR variation less than 2.5% in the range of 1530 nm to 1610 nm.
Surgical and per-oral endoscopic myotomy (POEM) for the treatment of primary esophageal motility disorders: A systematic analysis of current trends in Germany between 2011 and 2019
Authors: Kandler Jennis , Essing Tobias , Schöler David , Flügen Georg , Knoefel Wolfram T. , Roderburg Christoph , Luedde Tom , Loosen Sven H. 
Published: January 2024

Background/Aims
While surgery remains a standard treatment for primary esophageal motility disorders (PEMDs), per-oral endoscopic myotomy (POEM) has recently evolved as an alternative. Systematic data on current trends of invasive procedures for PEMDs in Germany are missing.

Methods
Hospital discharge data were used to evaluate trends and mortality of invasive treatment options for PEMDs in Germany between 2011 and 2019.

Results
4543 cases of PEMDs (achalasia: n = 4349, dyskinesia of the esophagus: n = 194) receiving open surgery (n = 200), minimal invasive surgery (n = 2366), or POEM (n = 1977) were identified. The relative proportion of POEM significantly increased from 10.9% (2011) to 65.7% (2019). Hospital mortality was 0.2%. The median duration of mechanical ventilation was significantly lower in POEM patients (29.4 hours) compared to open (274.0 hours) or minimal invasive (91.9 hours) surgery. The duration of hospitalization was lowest among POEM patients (5.7 days) compared to surgical procedures (13.7 and 7.7 days).

Conclusion
While the low in-hospital mortality of all procedures combined confirms the solid safety profile of invasive procedures in general, our findings show that POEM has the lowest duration of mechanical ventilation and hospitalization compared to invasive surgical options.