bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pelvic Venous Disorders: An Update in Terminology, Diagnosis, and Treatment
Authors: Clark Meghan R. , Taylor Amy C. 
Published: August 2023

AbstractPelvic venous disorder (PeVD) is a term that encompasses all the interrelated causes of chronic pelvic pain (CPP) and perineal/lower extremity varicose veins of pelvic venous origin historically known as nutcracker syndrome, pelvic congestion syndrome, and May-Thurner syndrome, resulting in a more precise diagnosis that accounts for the underlying pathophysiology and anatomy. PeVD manifests as CPP with associated vulvar and lower-extremity varicosities, left flank pain and hematuria, and lower extremity pain and swelling secondary to obstruction or reflux in the left renal, ovarian, or iliac veins. This article will focus specifically on the most current nomenclature, evaluation, and management of CPP of venous origin.
Recanalization of Proximal Fallopian Tube Obstruction in the Treatment of Infertility
Authors: Mody Priya , Salazar Gloria , Kohi Maureen P. 
Published: August 2023

AbstractInfertility affects approximately 15% of patients worldwide, with up to 40% of cases attributed to tubal disease, and up to 25% of those being proximal fallopian tube obstruction (FTO). Evaluation of tubal patency can be performed via laparoscopic chromopertubation, hysterosalpingography, or hysterosalpingo-contrast-sonography (HyCoSy). In patients with proximal tubal obstruction, fallopian tube recanalization (FTR) can result in up to 100% technical success rate with pregnancy rates of 12.8 to 51%. More pregnancies occur when oil-soluble contrast media are used versus water-soluble contrast media. Complications of FTR are rare and include tubal perforation, ectopic pregnancy, and pelvic infection. Reocclusion of fallopian tubes may occur in 20 to 50% of patients; however, FTR may be repeated in these cases. Overall, FTR is underutilized in the treatment of infertility secondary to proximal FTO and it can obviate costly and time-consuming assistive reproductive techniques such as in vitro fertilization in some patients, as well as decreasing physical and emotional stress.
The Role of Helicobacter pylori and Small Intestinal Bacterial Overgrowth in Parkinson's Disease
Authors: Justich Maria Belen , Rojas Olga L. , Fasano Alfonso 
Published: August 2023

AbstractParkinson's disease (PD) is a common neurodegenerative disorder whose etiology remains largely unexplained. Several studies have aimed to describe a causative effect in the interactions between the gastrointestinal tract and the brain, for both PD pathogenesis and disease course. However, the results have been controversial. Helicobacter pylori and small intestinal bacterial overgrowth (SIBO) are theorized to be agents capable of triggering chronic proinflammatory changes with a possible neurotoxic effect, as well as a cause of erratic L-dopa response in PD patients. This review evaluates the individual and possibly synergistic influence of H. pylori and SIBO on PD, to provide an opportunity to consider prospective therapeutic approaches.
What Factors Influence the Final Outcome in Occipital Condyle Fractures?
Authors: Srinivasan U. S. , Sultan Al-Busaidi Ali , Mubarak Eltayeb Abdalla Ali 
Published: August 2023

Abstract
Introduction Diagnosis of occipital condyle fracture (OCF) following a trauma needs high awareness among the trauma surgeons.
Aim In our study, we attempt to discern if any factor or a combination of factors influences the final outcome following OCF.
Materials and Methods We prospectively analyzed the outcome in OCF patients admitted during 2017 to 2019 at our center. We had 14 patients with polytrauma with OCF. Among them two were lost for follow-up. So, 12 patients were followed up for 6 months after injury. The following 10 factors were analyzed—age, sex, injury, Glasgow Coma Scale, Injury Severity Score, spinal injury, associated injuries, blood pressure, medical conditions, and surgical intervention. Outcome was divided into good and poor outcomes. Chi-squared test was used. All these patients were treated conservatively for OCF for 3 months.
Results There was no significant factor, since p-value was greater than 0.05 for all variables. Only Injury Severity Score (0.091) was close to the significant p-value. Seven patients had severe head injuries and among them one died and four had the worst outcome. Among the five patients who had spinal injuries, only two had good outcomes.
Conclusion Our results indicate that the outcome following OCF is not determined by any single factor. Injury Severity Score comes close to determining the final outcome. This indicates that the overall patient management especially of associated injuries is the determining factor in the outcome in patients who had sustained OCF.
Challenging Management of an Acute Traumatic Carotid-Cavernous Fistula in a 2-Year-Old Child with Literature Review
Authors: Solis Frank , Macha Luis , Toledo Mauro , Gálvez Ricardo , Ecos Rosa 
Published: August 2023

AbstractTraumatic carotid-cavernous fistula (TCCF) is a rare occurrence in the pediatric population. However, the neurological sequelae of TCCF are associated with higher morbidity and mortality in pediatric patients. We report the case of a 2-year-old child with TCCF treated at a public hospital in Peru. The etiology of the injury was due to a fall of approximately 5 meters. The diagnosis was made based on the clinical picture and neuroimaging findings. The initial proposed treatment was performed with the hope of preserving the parent artery; however, due to persistence of the TCCF, embolization of the parent artery with coils and embolizing substance was performed. A literature review of similar cases was performed and identified eight cases in children under 10 years of age. Endovascular management of an acute TCCF is a challenge due to the high morbidity and mortality during the acute phase and can be complicated when other traumatic injuries are present. Maintaining the parent artery is important; however, when this is not possible, trapping the parent artery may provide an alternate option when appropriate collaterals exist.
How has the Covid-19 pandemic affected wheelchair users? Time-series analysis of the number of railway passengers in Tokyo
Authors: Arai Yuko , Niwa Yukari , Kusakabe Takahiko , Honma Kentaro 
Published: August 2023

AbstractThe Coronavirus disease 2019 (COVID-19) has posed ‘new barriers’ to people with disabilities (PwDs) who have already experienced many barriers to using public transportation. However, there is limited quantitative knowledge of how PwDs have been affected by the COVID-19 pandemic. This study investigated the impact of the COVID-19 pandemic on the use of public transportation by PwDs over time. Specifically, we analysed time-series data on wheelchair rail passenger numbers and all rail passenger numbers in Tokyo from April 2012 to December 2021. The impact of COVID-19 was more accurately assessed by excluding seasonal variations in the time-series, and two key findings were obtained. First, the change point for the decline in the number of passengers owing to the COVID-19 pandemic was March 2020, one month earlier than the declaration of the state of emergency. Second, using the time-series model, the actual and estimated values were compared, and we found that wheelchair rail passenger numbers reduced by approximately 20 percentage points on average compared with all rail passengers. Wheelchair rail passengers were more severely affected by the COVID-19 pandemic than all rail passengers. Based on previous studies, these findings demonstrated that opportunities to participate in society were disproportionately reduced for PwDs during the COVID-19 pandemic. This study’s quantitative data and the resulting conclusions on wheelchair users are useful for inclusive planning for mitigating the pandemic’s impact by national administrations and public transport authorities.
Compartmentalizing Indigenous knowledge(s): binary framing and cognitive imperialism in social studies curriculum
Authors: Clarysse Liana Kibalenko 
Published: August 2023

AbstractThis qualitative analysis of the Social Studies curriculum for Grades 3 to 6 for the province of Ontario, Canada examines binary framing in curriculum as a mechanism of cognitive imperialism that compartmentalizes Indigenous knowledge(s). The following binaries are discussed: Positive/Negative; Conflict/Cooperation; and Us/Them in terms of the ways that they compartmentalize Indigenous knowledge(s) and reinforce cognitive imperialism. Themes for further research are noted including presumptions of neutrality that divorce power analysis from perspective-taking, the prioritizing of peaceful relations over redressing power imbalances and adding Indigenous-themed content to the curriculum is not enough. Recommendations for curriculum reform are indicated and decolonial justice education (DJE) is conceptualized for actionable steps towards answering the Calls to Action in the Truth and Reconciliation Commission of Canada (2015a, 2015b, 2015c).
Physical insights from imaginary-time density–density correlation functions
Authors: Dornheim Tobias , Moldabekov Zhandos A. , Tolias Panagiotis , Böhme Maximilian , Vorberger Jan 
Published: August 2023

An accurate theoretical description of the dynamic properties of correlated quantum many-body systems, such as the dynamic structure factor S(q, ω), is important in many fields. Unfortunately, highly accurate quantum Monte Carlo methods are usually restricted to the imaginary time domain, and the analytic continuation of the imaginary-time density–density correlation function F(q, τ) to real frequencies is a notoriously hard problem. Here, it is argued that often no such analytic continuation is required because by definition, F(q, τ) contains the same physical information as does S(q, ω), only represented unfamiliarly. Specifically, it is shown how one can directly extract key information such as the temperature or quasi-particle excitation energies from the τ domain, which is highly relevant for equation-of-state measurements of matter under extreme conditions [T. Dornheim et al., Nat. Commun. 13, 7911 (2022)]. As a practical example, ab initio path-integral Monte Carlo results for the uniform electron gas (UEG) are considered, and it is shown that even nontrivial processes such as the roton feature of the UEG at low density [T. Dornheim et al., Commun. Phys. 5, 304 (2022)] are manifested straightforwardly in F(q, τ). A comprehensive overview is given of various useful properties of F(q, τ) and how it relates to the usual dynamic structure factor. In fact, working directly in the τ domain is advantageous for many reasons and opens up multiple avenues for future applications.
Density and magnetic field strength dependence of radio pulses induced by energetic air showers
Authors: Ammerman-Yebra Juan , Alvarez-Muñiz Jaime , Zas Enrique 
Published: August 2023

Abstract
We have studied the effect of changing the density and magnetic field strength in the coherent pulses that are emitted as energetic showers develop in the atmosphere. For this purpose we have developed an extension of ZHS, a program to calculate coherent radio pulses from electromagnetic showers in homogeneous media, to account for the Lorentz force due to a magnetic field. This makes it possible to perform quite realistic simulations of radio pulses from air showers in a medium similar to the atmosphere but without variations of density with altitude. The effects of independently changing the density, the refractive index and the magnetic field strength are studied in the frequency domain for observers in the Cherenkov direction at far distances from the shower. This approach is particularly enlightening providing an explanation of the spectral behavior of the induced electric field in terms of shower development parameters. More importantly, it clearly displays the complex scaling properties of the pulses as density and magnetic field strength are varied. The usually assumed linear behavior of electric field amplitude with magnetic field strength is shown to hold up to a given magnetic field strength at which the extra time delays due to the deflection in the magnetic field break it. Scaling properties of the pulses are obtained as the density of air decreases relative to sea level. A remarkably accurate scaling law is obtained that relates the spectra of pulses obtained when reducing the density and increasing the magnetic field.
Comprehensive evaluation of methods for differential expression analysis of metatranscriptomics data
Authors: Cho Hunyong , Qu Yixiang , Liu Chuwen , Tang Boyang , Lyu Ruiqi , Lin Bridget M , Roach Jeffrey , Azcarate-Peril M Andrea , Aguiar Ribeiro Apoena , Love Michael I , Divaris Kimon , Wu Di 
Published: August 2023

Abstract
Understanding the function of the human microbiome is important but the development of statistical methods specifically for the microbial gene expression (i.e. metatranscriptomics) is in its infancy. Many currently employed differential expression analysis methods have been designed for different data types and have not been evaluated in metatranscriptomics settings. To address this gap, we undertook a comprehensive evaluation and benchmarking of 10 differential analysis methods for metatranscriptomics data. We used a combination of real and simulated data to evaluate performance (i.e. type I error, false discovery rate and sensitivity) of the following methods: log-normal (LN), logistic-beta (LB), MAST, DESeq2, metagenomeSeq, ANCOM-BC, LEfSe, ALDEx2, Kruskal–Wallis and two-part Kruskal–Wallis. The simulation was informed by supragingival biofilm microbiome data from 300 preschool-age children enrolled in a study of childhood dental disease (early childhood caries, ECC), whereas validations were sought in two additional datasets from the ECC study and an inflammatory bowel disease study. The LB test showed the highest sensitivity in both small and large samples and reasonably controlled type I error. Contrarily, MAST was hampered by inflated type I error. Upon application of the LN and LB tests in the ECC study, we found that genes C8PHV7 and C8PEV7, harbored by the lactate-producing Campylobacter gracilis, had the strongest association with childhood dental disease. This comprehensive model evaluation offers practical guidance for selection of appropriate methods for rigorous analyses of differential expression in metatranscriptomics. Selection of an optimal method increases the possibility of detecting true signals while minimizing the chance of claiming false ones.
A Bayesian model for genomic prediction using metabolic networks
Authors: Onogi Akio 
Published: August 2023

Abstract

Motivation
Genomic prediction is now an essential technique in breeding and medicine, and it is interesting to see how omics data can be used to improve prediction accuracy. Precedent work proposed a metabolic network-based method in biomass prediction of Arabidopsis; however, the method consists of multiple steps that possibly degrade prediction accuracy.

Results
We proposed a Bayesian model that integrates all steps and jointly infers all fluxes of reactions related to biomass production. The proposed model showed higher accuracies than methods compared both in simulated and real data. The findings support the previous excellent idea that metabolic network information can be used for prediction.

Availability and implementation
All R and stan scripts to reproduce the results of this study are available at https://github.com/Onogi/MetabolicModeling.
BEENE: deep learning-based nonlinear embedding improves batch effect estimation
Authors: Rahman Md Ashiqur , Tutul Abdullah Aman , Sharmin Mahfuza , Bayzid Md Shamsuzzoha 
Published: August 2023

Abstract

Motivation
Analyzing large-scale single-cell transcriptomic datasets generated using different technologies is challenging due to the presence of batch-specific systematic variations known as batch effects. Since biological and technological differences are often interspersed, detecting and accounting for batch effects in RNA-seq datasets are critical for effective data integration and interpretation. Low-dimensional embeddings, such as principal component analysis (PCA) are widely used in visual inspection and estimation of batch effects. Linear dimensionality reduction methods like PCA are effective in assessing the presence of batch effects, especially when batch effects exhibit linear patterns. However, batch effects are inherently complex and existing linear dimensionality reduction methods could be inadequate and imprecise in the presence of sophisticated nonlinear batch effects.

Results
We present Batch Effect Estimation using Nonlinear Embedding (BEENE), a deep nonlinear auto-encoder network which is specially tailored to generate an alternative lower dimensional embedding suitable for both linear and nonlinear batch effects. BEENE simultaneously learns the batch and biological variables from RNA-seq data, resulting in an embedding that is more robust and sensitive than PCA embedding in terms of detecting and quantifying batch effects. BEENE was assessed on a collection of carefully controlled simulated datasets as well as biological datasets, including two technical replicates of mouse embryogenesis cells, peripheral blood mononuclear cells from three largely different experiments and five studies of pancreatic islet cells.

Availability and implementation
BEENE is freely available as an open source project at https://github.com/ashiq24/BEENE.
Defining the cellular complexity of the zebrafish bipotential gonad
Authors: Kossack Michelle E , Tian Lucy , Bowie Kealyn , Plavicki Jessica S 
Published: August 2023

Abstract
Zebrafish are routinely used to model reproductive development, function, and disease, yet we still lack a clear understanding of the fundamental steps that occur during early bipotential gonad development, including when endothelial cells, pericytes, and macrophage arrive at the bipotential gonad to support gonad growth and differentiation. Here, we use a combination of transgenic reporters and single-cell sequencing analyses to define the arrival of different critical cell types to the larval zebrafish gonad. We determined that blood initially reaches the gonad via a vessel formed from the swim bladder artery, which we have termed the gonadal artery. We find that vascular and lymphatic development occurs concurrently in the bipotential zebrafish gonad and our data suggest that similar to what has been observed in developing zebrafish embryos, lymphatic endothelial cells in the gonad may be derived from vascular endothelial cells. We mined preexisting sequencing datasets to determine whether ovarian pericytes had unique gene expression signatures. We identified 215 genes that were uniquely expressed in ovarian pericytes, but not expressed in larval pericytes. Similar to what has been shown in the mouse ovary, our data suggest that pdgfrb+ pericytes may support the migration of endothelial tip cells during ovarian angiogenesis. Using a macrophage-driven photoconvertible protein, we found that macrophage established a nascent resident population as early as 12 dpf and can be observed removing cellular material during gonadal differentiation. This foundational information demonstrates that the early bipotential gonad contains complex cellular interactions, which likely shape the health and function of the mature gonad.
Neural, physiological and behavioural correlates of empathy for pain in Tourette syndrome
Authors: Weiblen Ronja , Robert Carina , Petereit Pauline , Heldmann Marcus , Münte Thomas F , Münchau Alexander , Müller-Vahl Kirsten , Krämer Ulrike M 
Published: August 2023

Abstract
Persons with Tourette syndrome show altered social behaviours, such as echophenomena and increased personal distress in emotional situations. These symptoms may reflect an overactive mirror neuron system, causing both increased automatic imitation and a stronger tendency to share others’ emotions. To test this, we measured the individual level of echophenomena with a video protocol and experimentally induced empathy for pain in 21 participants with Tourette syndrome and 25 matched controls. In the empathy for pain paradigm, pictures of hands and feet in painful or neutral situations were presented, while we measured participants’ EEG and skin conductance response. Changes in somatosensory mu suppression during the observation of the pictures and pain ratings were compared between groups, and correlations were calculated with the occurrence of echophenomena, self-reported empathy and clinical measures. Our Tourette syndrome sample showed significantly more echophenomena than controls, but the groups showed no behavioural differences in empathic abilities. However, controls, but not patients with Tourette syndrome, showed the predicted increased mu suppression when watching painful compared to neutral actions. While echophenomena were present in all persons with Tourette syndrome, the hypothesis of an overactive mirror neuron system in Tourette syndrome could not be substantiated. On the contrary, the Tourette syndrome group showed a noticeable lack of mu attenuation in response to pain stimuli. In conclusion, we found a first hint of altered processing of others’ emotional states in a brain region associated with the mirror neuron system.
Digital fingerprinting for identifying malicious collusive groups on Twitter
Authors: Ikwu Ruth , Giommoni Luca , Javed Amir , Burnap Pete , Williams Matthew 
Published: August 2023

Abstract
Propagation of malicious code on online social networks (OSNs) is often a coordinated effort by collusive groups of malicious actors hiding behind multiple online identities (or digital personas). Increased interaction in OSN has made them reliable for the efficient orchestration of cyberattacks such as phishing click bait and drive-by downloads. URL shortening enables obfuscation of such links to malicious websites and massive interaction with such embedded malicious links in OSN guarantees maximum reach. These malicious links lure users to malicious endpoints where attackers can exploit system vulnerabilities. Identifying the organized groups colluding to spread malware is non-trivial owing to the fluidity and anonymity of criminal digital personas on OSN. This paper proposes a methodology for identifying such organized groups of criminal actors working together to spread malicious links on OSN. Our approach focuses on understanding malicious users as ‘digital criminal personas’ and characteristics of their online existence. We first identify those users engaged in propagating malicious links on OSN platforms, and further develop a methodology to create a digital fingerprint for each malicious OSN account/digital persona. We create similarity clusters of malicious actors based on these unique digital fingerprints to establish ‘collusive’ behaviour. We evaluate the ability of a cluster-based approach on OSN digital fingerprinting to identify collusive behaviour in OSN by estimating within-cluster similarity measures and testing it on a ground-truth dataset of five known colluding groups on Twitter. Our results show that our digital fingerprints can identify 90% of cyber personas engaged in collusive behaviour and 75% of collusion in a given sample set.
MineProt: a stand-alone server for structural proteome curation
Authors: Zhu Yunchi , Tong Chengda , Zhao Zuohan , Lu Zuhong 
Published: August 2023

Abstract
AlphaFold-like systems are rapidly expanding the scale of proteome structuring, and MineProt provides an effective solution for custom curation of these novel high-throughput data. It enables researchers to build their own server in simple steps, run almost out-of-the-box scripts to annotate and curate their proteins, analyze their data via a user-friendly online interface, and utilize plugins to extend the functionality of server. It is expected to support researcher productivity and facilitate data sharing in the new era of structural proteomics.
Database URL MineProt is open-source software available at https://github.com/huiwenke/MineProt.