bluuebunny/crossref_metadata_2025 huggingface dataset:
ctGAN: combined transformation of gene expression and survival data with generative adversarial network
Authors: Kim Jaeyoon , Seok Junhee
Published: July 2024

Recent studies have extensively used deep learning algorithms to analyze gene expression to predict disease diagnosis, treatment effectiveness, and survival outcomes. Survival analysis studies on diseases with high mortality rates, such as cancer, are indispensable. However, deep learning models are plagued by overfitting owing to the limited sample size relative to the large number of genes. Consequently, the latest style-transfer deep generative models have been implemented to generate gene expression data. However, these models are limited in their applicability for clinical purposes because they generate only transcriptomic data. Therefore, this study proposes ctGAN, which enables the combined transformation of gene expression and survival data using a generative adversarial network (GAN). ctGAN improves survival analysis by augmenting data through style transformations between breast cancer and 11 other cancer types. We evaluated the concordance index (C-index) enhancements compared with previous models to demonstrate its superiority. Performance improvements were observed in nine of the 11 cancer types. Moreover, ctGAN outperformed previous models in seven out of the 11 cancer types, with colon adenocarcinoma (COAD) exhibiting the most significant improvement (median C-index increase of ~15.70%). Furthermore, integrating the generated COAD enhanced the log-rank p-value (0.041) compared with using only the real COAD (p-value = 0.797). Based on the data distribution, we demonstrated that the model generated highly plausible data. In clustering evaluation, ctGAN exhibited the highest performance in most cases (89.62%). These findings suggest that ctGAN can be meaningfully utilized to predict disease progression and select personalized treatments in the medical field.
LDER-GE estimates phenotypic variance component of gene–environment interactions in human complex traits accurately with GE interaction summary statistics and full LD information
Authors: Dong Zihan , Jiang Wei , Li Hongyu , DeWan Andrew T , Zhao Hongyu
Published: July 2024

Gene–environment (GE) interactions are essential in understanding human complex traits. Identifying these interactions is necessary for deciphering the biological basis of such traits. In this study, we review state-of-art methods for estimating the proportion of phenotypic variance explained by genome-wide GE interactions and introduce a novel statistical method Linkage-Disequilibrium Eigenvalue Regression for Gene–Environment interactions (LDER-GE). LDER-GE improves the accuracy of estimating the phenotypic variance component explained by genome-wide GE interactions using large-scale biobank association summary statistics. LDER-GE leverages the complete Linkage Disequilibrium (LD) matrix, as opposed to only the diagonal squared LD matrix utilized by LDSC (Linkage Disequilibrium Score)-based methods. Our extensive simulation studies demonstrate that LDER-GE performs better than LDSC-based approaches by enhancing statistical efficiency by ~23%. This improvement is equivalent to a sample size increase of around 51%. Additionally, LDER-GE effectively controls type-I error rate and produces unbiased results. We conducted an analysis using UK Biobank data, comprising 307 259 unrelated European-Ancestry subjects and 966 766 variants, across 217 environmental covariate-phenotype (E-Y) pairs. LDER-GE identified 34 significant E-Y pairs while LDSC-based method only identified 23 significant E-Y pairs with 22 overlapped with LDER-GE. Furthermore, we employed LDER-GE to estimate the aggregated variance component attributed to multiple GE interactions, leading to an increase in the explained phenotypic variance with GE interactions compared to considering main genetic effects only. Our results suggest the importance of impacts of GE interactions on human complex traits.
An acidic loop in the forkhead-associated domain of the yeast meiosis-specific kinase Mek1 interacts with a specific motif in a subset of Mek1 substrates
Authors: Weng Qixuan , Wan Lihong , Straker Geburah C , Deegan Tom D , Duncker Bernard P , Neiman Aaron M , Luk Ed , Hollingsworth Nancy M
Published: July 2024

The meiosis-specific kinase Mek1 regulates key steps in meiotic recombination in the budding yeast, Saccharomyces cerevisiae. MEK1 limits resection at double-strand break (DSB) ends and is required for preferential strand invasion into homologs, a process known as interhomolog bias. After strand invasion, MEK1 promotes phosphorylation of the synaptonemal complex protein Zip1 that is necessary for DSB repair mediated by a crossover-specific pathway that enables chromosome synapsis. In addition, Mek1 phosphorylation of the meiosis-specific transcription factor, Ndt80, regulates the meiotic recombination checkpoint that prevents exit from pachytene when DSBs are present. Mek1 interacts with Ndt80 through a 5-amino acid sequence, RPSKR, located between the DNA-binding and activation domains of Ndt80. AlphaFold Multimer modeling of a fragment of Ndt80 containing the RPSKR motif and full-length Mek1 indicated that RPSKR binds to an acidic loop located in the Mek1 FHA domain, a noncanonical interaction with this motif. A second protein, the 5′-3′ helicase Rrm3, similarly interacts with Mek1 through an RPAKR motif and is an in vitro substrate of Mek1. Genetic analysis using various mutants in the MEK1 acidic loop validated the AlphaFold model, in that they specifically disrupt 2-hybrid interactions with Ndt80 and Rrm3. Phenotypic analyses further showed that the acidic loop mutants are defective in the meiotic recombination checkpoint and, in certain circumstances, exhibit more severe phenotypes compared to the NDT80 mutant with the RPSKR sequence deleted, suggesting that additional, as yet unknown, substrates of Mek1 also bind to Mek1 using an RPXKR motif.
Combination of 2 Quantitative Immunoassays and Clinical Score Algorithm to Reduce False-Negative Results in Heparin-Induced Thrombocytopenia: Prevalence Study of Mauriziano Hospital in Turin, Italy
Authors: Minei Veronica , Valesella Paolo , Papandrea Maria , Sivera Piera , Insana Antonio , Cosseddu Domenico , Umurungi Johanna , Montaruli Barbara
Published: July 2024

Background

Heparin-induced thrombocytopenia (HIT) is a serious adverse effect of heparin treatment caused by platelet-activating anti-platelet factor 4 (PF4)/heparin antibodies. Accurate diagnosis of HIT is essential but remains challenging. The aim of our study was to explore the performance of our optimized diagnostic laboratory algorithm, based on Chemiluminescence (CliA) and ELISA immunoassays, on suspected HIT patients. The study compared the prevalence of HIT diagnosis in A.O. Mauriziano with the literature.

Methods

163 consecutive patients were investigated for suspected HIT with CliA HemosIL Acustar HIT-IgG, Werfen. HIT was ruled out in all patients with CliA <0.13 U/mL. All patients with CliA >0.13 U/mL were further investigated with Zymutest-HIA anti-PF4 IgG ELISA immunoassay. In these patients, HIT was ruled out on the combination of CliA between 0.13 and 1.0 U/mL followed by ELISA assay <0.300 OD. HIT was ruled in patients whose plasma tested positive or doubtful with CliA and positive with ELISA immunoassay and confirmed positive with a platelet aggregation test (PAT). Suspicion of HIT was revealed with clinical 4Ts score or recent suggestive anamnestic history.

Results

Our diagnostic algorithm ruled out HIT diagnosis in 144/163 patients (88%) and predicted a positive PAT in 5/19 (26%) of CliA positive (4/5) or ELISA positive and CliA doubtful (1/5) patients.

Conclusions

Our prevalence was 3.1%, comparable with the literature. The approach combining 2 quantitative immunoassays’ (CliA and ELISA) results and 4Ts score probability was able to rule out the diagnosis within 1 h in 66% of patients with suspected HIT and within 24 h in 88% of patients. In the remaining 12% of cases, management decisions have to be based on individualized judgment while awaiting functional confirming results (48–72 h).
Genital Burns Are Associated With Worse Psychosocial and Physical Outcomes
Authors: Shah Suhaib , Golovko George , Karim Abbas , Segura Carolina , Song Juquan , Haseem Maria , Wolf Steven , El Ayadi Amina
Published: July 2024

Genital burns are unique and complex injuries that impact patients physically and emotionally. This study investigates the specific impact of genital burns on psychosocial and physical outcomes. A retrospective cohort study was conducted using the TriNetX database, encompassing over 117 million patients from U.S. healthcare institutions. Patients with genital burns were identified and categorized into subcohorts based on total body surface area (TBSA) and burn degree. Propensity score matching and cohort balancing were performed based on age, gender, race, and ethnicity. Outcomes were analyzed both short-term (1 month) and long-term (5 years), focusing on psychiatric and physical aspects. This study identified 3496 genital burn patients over a 15-year period. Analyses revealed that genital burns significantly increased short-term risk of death (risk ratios [RR]: 2.8), anxiety (RR: 2.656), hospitalization (RR: 2.167), and any anxiety, posttraumatic stress disorder, or depression (RR: 2.363), and long-term risk of death (RR: 1.658) and pruritus (RR: 1.58) (all P < .05). Interestingly, genital burn patients showed a lower risk of chronic joint pain compared to other burn injuries (RR: 0.815) (P < .05). These results occurred independently of the extent of TBSA. Genital burns have a distinctive impact on patients, leading to higher rates of certain psychiatric morbidities and physical complications. This study highlights the need for tailored care and consideration of the unique challenges faced by patients with genital burns, both in the immediate aftermath and in the long term. Understanding the specific impacts of genital burns is vital for healthcare practitioners to develop care strategies and better support for patients recovering from such injuries.
Antibiotic dip and irrigation solutions confer increased antimicrobial efficacy of inflatable penile prosthesis hydrophilic surfaces compared with 0.05% chlorhexidine gluconate
Authors: Simhal Rishabh , Im Brian H , Shah Sohan , Guillaume Samone , Kerkvliet Carlos Perez , Evans Rachel , Hickok Noreen J , Chung Paul H
Published: July 2024

Background

Chlorhexidine gluconate (CHG) (0.05%) has recently been suggested as both a dip for the hydrophilic surface and an irrigation solution in the setting of penile prosthesis (PP) surgery.

Aim

The study sought to compare the antimicrobial efficacy of 0.05% CHG with vancomycin and gentamicin (VG) antibiotics as dip and/or irrigation solutions in the setting of a hydrophilic PP surface in vitro.

Methods

Sterile PPs with a hydrophilic coating were obtained. A series of experiments were performed to evaluate the efficacy of normal saline (NS), 0.05% CHG, or VG as dip and/or irrigation solutions to reduce methicillin-sensitive Staphylococcus aureus adhesion to PP surfaces. The 8-mm discs from PPs were incubated in 105 colony-forming units/mL of methicillin-sensitive S aureus for 48 hours, plated, and counted. Disc-diffusion tests were conducted by suspending 6-mm discs for 2 minutes in NS, 0.05% CHG, or VG, then placing them coated side down onto plates streaked with the following organisms: methicillin-sensitive S aureus, S epidermidis, Enterococcus, and Escherichia coli. After 24 hours of growth, zones of inhibition were measured.

Outcomes

We found average bacterial counts (colony-forming units/mL) and zones of inhibition (mm) following a series of treatment protocols of PP discs.

Results

PP discs dipped in VG reduced bacterial adhesion to the implant surface >0.05% CHG (~5.5 log vs ~1.5 log; P < .01). Discs irrigated with either 0.05% CHG or NS removed all dip solution adsorbed to the hydrophilic surface, allowing bacterial growth. VG irrigation adsorbed to the hydrophilic surface even after 0.05% CHG or NS dips, reducing bacterial adherence (~3 log). Dipping and irrigating discs with VG was most effective in reducing adherent bacteria (~5.5 log) and was the only irrigation that showed antimicrobial activity.

Clinical Translation

VG, when used both as a prophylactic dip and as an intraoperative irrigation solution for hydrophilic penile implant surfaces, has improved efficacy to 0.05% CHG and NS.

Strengths and Limitations

This is the first study to compare the use of VG, 0.05% CHG, and NS as prophylactic dips and intraoperative irrigations for hydrophilic penile implant surfaces. Limitations include the use of in vitro studies, which serve as a proxy for in vivo practices and may not be entirely accurate nor translatable clinically.

Conclusion

We demonstrated the superior efficacy of VG as a combined dip and irrigation solution for hydrophilic penile implant surfaces compared with 0.05% CHG.
Ribosome specialization in cancer: a spotlight on ribosomal proteins
Authors: Ramalho Sofia , Dopler Anna , Faller William James
Published: July 2024

In the past few decades, our view of ribosomes has changed substantially. Rather than passive machines without significant variability, it is now acknowledged that they are heterogeneous, and have direct regulatory capacity. This ‘ribosome heterogeneity’ comes in many flavors, including in both the RNA and protein components of ribosomes, so there are many paths through which ribosome specialization could arise. It is easy to imagine that specialized ribosomes could have wide physiological roles, through the translation of specific mRNA populations, and there is now evidence for this in several contexts. Translation is highly dysregulated in cancer, needed to support oncogenic phenotypes and to overcome cellular stress. However, the role of ribosome specialization in this is not clear. In this review we focus on specialized ribosomes in cancer. Specifically, we assess the impact that post-translational modifications and differential ribosome incorporation of ribosomal proteins (RPs) have in this disease. We focus on studies that have shown a ribosome-mediated change in translation of specific mRNA populations, and hypothesize how such a process could be driving other phenotypes. We review the impact of RP-mediated heterogeneity in both intrinsic and extrinsic oncogenic processes, and consider how this knowledge could be leveraged to benefit patients.
A swallowed denture leading to misdiagnosis with esophageal neoplasm: a case report
Authors: Shadidi Asil Roozbeh , Zamani Amir , Fooladi Zahra , Hatampour Kasra
Published: July 2024

Introduction

Foreign body ingestion can lead to esophageal complications, including perforation and impaction, in up to 20% of cases, making it a critical situation. Misdiagnosis or delayed diagnosis can cause severe complications.

Case presentation

We present the case of a 78-year-old female who swallowed an acrylic partial denture leading to progressive dysphagia and a vegetative ulcerative lesion on endoscopy. The lesion was initially misdiagnosed as a neoplasm of the esophagus. CT scan and a repeat endoscopy revealed the presence of a denture in the esophagus. The denture was successfully removed with a rigid esophagoscope, and no evidence of complications was reported in follow-up visits.

Discussion

Diagnosis of esophageal foreign bodies involves imaging studies and endoscopy, which is the gold standard for diagnosis and management. CT scans also have an important role in diagnosing controversial cases. Treatment depends on the size, shape, and location of the object.
Automatic purification of skylight spectrum based on an autoencoder
Authors: Ding Zhichao , Tu Liangping , Yang Haifeng , Jiang Bin , Li Xiangru , Yang Yuqing , Zhang Hui , Li Jundi
Published: July 2024

In the realm of astronomical spectroscopic observation, the purity of skylight spectra is crucial for accurate analysis, often complicated by interference from neighboring celestial objects. Addressing this challenge, a novel automatic purification algorithm is proposed in this study, leveraging the power of auto-coding mechanisms. By harnessing the inherent data features and shared representations between skylight and target objects, this method effectively isolates skylight spectra from residual signals of neighboring objects. Central to this approach is the utilization of an encoder-decoder framework. The encoder dynamically learns the combined features of skylight and target objects, generating respective coding vectors. These vectors are then utilized to subtract the target-specific features from the skylight coding space, facilitating the extraction of pure skylight characteristics. Subsequently, the decoder reconstructs the refined skylight data, effectively eliminating residual components associated with neighboring celestial bodies. A notable strength of this algorithm lies in its ability to perform feature extraction and purification autonomously, without relying on labeled data. Experimental validation conducted on LAMOST-DR5 datasets demonstrates the efficacy of the proposed method. By effectively removing spectral information from target objects within skylight spectra, the algorithm yields comparatively pure skylight spectra, paving the way for enhanced astronomical spectroscopic analyses.
Predicting Clinical Improvement in Early Psychosis Using Circuit-Based Resting-State Functional Magnetic Resonance Imaging
Authors: Smucny Jason , Lesh Tyler A , Albuquerque Marina D , Rhilinger Joshua P , Carter Cameron S
Published: July 2024

Background and Hypothesis

Identifying biomarkers that predict treatment response in early psychosis (EP) is a priority for psychiatry research. Previous work suggests that resting-state connectivity biomarkers may have promise as predictive measures, although prior results vary considerably in direction and magnitude. Here, we evaluated the relationship between intrinsic functional connectivity of the attention, default mode, and salience resting-state networks and 12-month clinical improvement in EP.

Study Design

Fifty-eight individuals with EP (less than 2 years from illness onset, 35 males, average age 20 years) had baseline and follow-up clinical data and were included in the final sample. Of these, 30 EPs showed greater than 20% improvement in Brief Psychiatric Rating Scale (BPRS) total score at follow-up and were classified as “Improvers.”

Study Results

The overall logistic regression predicting Improver status was significant (χ2 = 23.66, Nagelkerke’s R2 = 0.45, P < .001, with 85% concordance). Significant individual predictors of Improver status included higher default mode within-network connectivity, higher attention-default mode between-network connectivity, and higher attention-salience between-network connectivity. Including baseline BPRS as a predictor increased model significance and concordance to 92%, and the model was not significantly influenced by the dose of antipsychotic medication (chlorpromazine equivalents). Linear regression models predicting percent change in BPRS were also significant.

Conclusions

Overall, these results suggest that resting-state functional magnetic resonance imaging connectivity may serve as a useful biomarker of clinical outcomes in recent-onset psychosis.
Overview of multifunctional Tregs in cardiovascular disease: From insights into cellular functions to clinical implications
Authors: Kumar Vipin , Narisawa Megumi , Cheng Xian Wu
Published: July 2024

Regulatory T cells (Tregs) are crucial in regulating T‐cell‐mediated immune responses. Numerous studies have shown that dysfunction or decreased numbers of Tregs may be involved in inflammatory cardiovascular diseases (CVDs) such as atherosclerosis, hypertension, myocardial infarction, myocarditis, cardiomyopathy, valvular heart diseases, heart failure, and abdominal aortic aneurysm. Tregs can help to ameliorate CVDs by suppressing excessive inflammation through various mechanisms, including inhibition of T cells and B cells, inhibition of macrophage‐induced inflammation, inhibition of dendritic cells and foam cell formation, and induction of anti‐inflammatory macrophages. Enhancing or restoring the immunosuppressive activity of Tregs may thus serve as a fundamental immunotherapy to treat hypertension and CVDs. However, the precise molecular mechanisms underlying the Tregs‐induced protection against hypertension and CVDs remain to be investigated. This review focuses on recent advances in our understanding of Tregs subsets and function in CVDs. In addition, we discuss promising strategies for using Tregs through various pharmacological approaches to treat hypertension and CVDs.
The Effects of Mentoring Programs on Mental Health in Undergraduate Nursing Students: An Integrative Review
Authors: Skrovanek Elizabeth , Karakachian Angela , Nolfi David
Published: July 2024

AIM

The aim of this study was to examine the effects of mentoring programs on undergraduate nursing students’ mental health.

BACKGROUND

The study of nursing has been cited as stressful, with negative effects on academic and physical well-being and mental health in nursing students.

METHOD

An integrative review of the literature using the method of Whittemore and Knafl was performed on mentoring programs designed to mitigate student stress. Electronic databases searched included CINAHL, Medline, PubMed, Embase, ERIC, and Scopus.

RESULTS

The eight studies included in this review suggest that mentoring has positive impacts on nursing students’ mental health, reducing stress and anxiety and enhancing well-being and sense of belonging.

CONCLUSION

Mentoring programs have positive effects on mental health outcomes in undergraduate nursing students. Implementation of structured programs at the start of undergraduate studies can facilitate increased mental and physical well-being and decrease stress and anxiety.
Impact of Patient Race/Ethnicity on Premium Intraocular Lens Utilization
Authors: Solli Elena M. , Prescott Christina R.
Published: July 2024

Objectives:

To evaluate the relationship between social determinants of health and the likelihood of receiving a premium intraocular lens (IOL) at the time of cataract surgery.

Methods:

Retrospective chart review of a single-center, academic ophthalmology practice over a one-year period, with a primary outcome measure of placement of either a premium or standard IOL. We used logistic regression to calculate the odds of receiving a premium IOL, stratifying patients based on self-identified race/ethnicity, age, sex, insurance type (private insurance vs. Medicare or Medicaid), estimated household income (based on median household income for zip code), and presence of ocular pathology.

Results:

Compared with self-identified White patients, Black patients were least likely to receive premium IOLs (OR=0.220, 95% CI 0.137–0.340, P<0.001), followed by Hispanic patients (OR=0.308, 95% CI 0.104–0.730) and Asian patients (OR=0.479, 95% CI 0.302–0.734). Patients with Medicare or Medicaid insurance were also less likely to receive premium IOLs (OR 0.522, 95% CI 0.336–0.784).

Conclusions:

White patients in our practice were more likely to receive premium IOLs than non-White patients, even when controlling for age, sex, insurance type, estimated median household income, and presence of ocular comorbidities. The underlying reason for this disparity should be explored further.
Utilization of Discharge Checklist and Improved Education Reduces Hospital Readmission Rates in Childhood Leukemia Patients Receiving Induction Therapy
Authors: Goode Erin , Fishel Ben-Kenan Rotem , Hess Jennifer , Walsh Alexandra
Published: July 2024

Objective:

The aim is to identify preventable cause for hospital readmissions during induction and implement interventions to decreased preventable treatment-associated complications.

Background:

Multiple factors contribute to patients with acute lymphoblastic leukemia (ALL) requiring readmissions during induction.

Materials and Methods:

A dashboard monitored features of newly diagnosed patients with ALL. Readmission causes were stratified as preventable, possibly preventable, or unpreventable. A discharge checklist, including standardized education, and change of discharge date were implemented.

Results:

Initially, there were 57 hospital readmissions of 98 patients (9 intensive care unit admissions and 2 deaths). Sixteen preventable (28.1%) and 32 unpreventable (56.1%) readmissions. After the interventions were initiated, including improved education, discharge checklist utilization, and standardized discharge date, there were 23 readmissions (78.3% were unpreventable, 6 intensive care unit admissions).

Conclusion:

Intervention implementation reduced readmission rates of induction patients with ALL by 20%.
Spinal Atypical Teratoid Rhabdoid Tumor in a 14-year-old Child With Down Syndrome: A Case Report
Authors: Zahid Soha , Bashir Farrah , Minhas Khurram , Anwar Shayan Seerat , Javed Gohar , Hawkins Cynthia , Bouffet Eric , Mushtaq Naureen
Published: July 2024

Individuals with 21 trisomy or Down syndrome (DS) are known to have an increased risk of acute leukemia, while they rarely develop solid or central nervous system (CNS) tumors. Atypical teratoid rhabdoid tumor (ATRT) is a highly aggressive CNS-WHO grade 4 neoplasm, which has never been reported in association with Down syndrome. We present a case study of a 14-year-old female with Down syndrome, diagnosed with intradural-extramedullary spinal ATRT. The chief complaints included bilateral lower limb weakness, constipation, and urinary incontinence for 2 weeks. Surgery was scheduled, and a biopsy was taken. The histopathology, immunohistochemistry, and molecular analysis confirmed the diagnosis of the ATRT-MYC/group 2B subgroup. This report highlights the challenges of managing a patient with complex medical conditions. Moreover, it adds to the existing literature on CNS tumors in patients with Down syndrome.
Intraoperative Measurement-Based Approach to Supratip Deformity in Open Structural Rhinoplasty
Authors: Şibar Serhat , Erdal Ayhan Işık , Doruk Mert , Gündüz Nurullah , Özçiler Mehmet Fatih
Published: July 2024

Background

Supratip deformity is one of the most common complications after open rhinoplasty. This study aimed to define a new risk scoring system for supratip deformity and determine the distances that should be left between the tip defining point (TDP) and anterior septal angle (ASA) to prevent it.

Methods

Four hundred sixty-nine patients who underwent open rhinoplasty between 2018–2022 were included in this retrospective study. The patients were evaluated according to the risk scoring system consisting of four parameters (skin thickness, lower lateral cartilage anatomy, amount of hump resection, and soft tissue procedures). Because of the presence of supratip deformity at the postoperative 12th month, the patients were divided into two groups: (i) without supratip deformity (n = 418) and (ii) with supratip deformity (n = 51). Statistical inferences were made regarding the development of supratip deformity by evaluating the relationship between the risk scores and the intraoperative TDP-ASA distances.

Results

There was a significant difference between the groups in risk scores (P < 0.05). In cases with high-risk scores, it was calculated that the probability of developing supratip deformity decreased significantly when the TDP-ASA distance was above 7.5 mm and increased significantly when the TDP-ASA distance was below 6.5 mm. In cases with low-risk scores, it was found that the probability of developing supratip deformity was reduced considerably when the TDP-ASA distance was over 6.0 mm.

Conclusions

The authors recommend keeping the TDP-ASA distance above 6.0 mm in low-risk patients and 7.5 mm in high-risk patients to avoid supratip deformity.
Response to Intermittent Theta Burst Stimulation in Treatment-Resistant Depression
Authors: Tonkul Mustafa , Baune Bernhard T. , Kavakbasi Erhan
Published: July 2024

Introduction

Intermittent theta burst stimulation (iTBS) is a novel form of repetitive transcranial magnetic stimulation (rTMS) conducted in patients with treatment-resistant depression (TRD). In this retrospective naturalistic study, we investigated the outcome of iTBS in treatment-resistant depression patients with (ECT+) and without (ECT−) history of electroconvulsive therapy (ECT) in their current depressive episode, as well as among previous ECT responders and nonresponders.

Methods

We included 66 inpatients (57.6% women; mean age, 52.7 years) at a German University Department of Psychiatry. A binary logistic regression model was utilized to investigate the impact of ECT treatment history on response to iTBS.

Results

Overall response rate was 51.5%. History of ECT in the current episode was present in 47% of patients. In the regression model, history of ECT in the current episode was associated with significantly worse response to iTBS (odds ratio, 0.252; 95% confidence interval, 0.085–0.743; P = 0.013), whereas other disease- and treatment-related covariates had no significant impact on treatment outcome. In the ECT+ group, ECT nonresponders showed a significantly worse outcome of iTBS than ECT responders. Overall rate of treatment discontinuations was 3%.

Conclusions

In this study, iTBS was most effective in patients without history of ECT in the current episode. Previous ECT responders had better outcome following iTBS than ECT nonresponders. Hence, patients with ECT response, who had to discontinue ECT due to side effects or complications, may be considered suitable candidates to be switched to iTBS.
Co-designing a wiki-based community knowledge management system for personal science
Authors: Kloppenborg Katharina , Price Ball Mad , Jonas Steven , Wolf Gary Isaac , Greshake Tzovaras Bastian
Published: July 2024

Personal science is the practice of addressing personally relevant health questions through self-research. Implementing personal science can be challenging, owing to the need to develop and adopt research protocols, tools and methods. While online communities can provide valuable peer support, tools for systematically accessing community knowledge are lacking. The objective of this study is to apply a participatory design process involving a community of personal science practitioners to develop a peer-produced knowledge base that supports the needs of practitioners as consumers and contributors of knowledge. The process led to the development of the Personal Science Wiki, an open repository for documenting and accessing individual self-tracking projects while facilitating the establishment of consensus knowledge. After initial design iterations and a field testing phase, we performed a user study with 21 participants to test and improve the platform, and to explore suitable information architectures. The study deepened our understanding of barriers to scaling the personal science community, established an infrastructure for knowledge management actively used by the community and provided lessons on challenges, information needs, representations and architectures to support individuals with their personal health inquiries.
Vocal repertoire and individuality in the plains zebra (
Equus quagga
)
Authors: Xie Bing , Daunay Virgile , Petersen Troels C. , Briefer Elodie F.
Published: July 2024

Acoustic signals are vital in animal communication, and quantifying them is fundamental for understanding animal behaviour and ecology. Vocalizations can be classified into acoustically and functionally or contextually distinct categories, but establishing these categories can be challenging. Newly developed methods, such as machine learning, can provide solutions for classification tasks. The plains zebra is known for its loud and specific vocalizations, yet limited knowledge exists on the structure and information content of its vocalzations. In this study, we employed both feature-based and spectrogram-based algorithms, incorporating supervised and unsupervised machine learning methods to enhance robustness in categorizing zebra vocalization types. Additionally, we implemented a permuted discriminant function analysis to examine the individual identity information contained in the identified vocalization types. The findings revealed at least four distinct vocalization types—the ‘snort’, the ‘soft snort’, the ‘squeal’ and the ‘quagga quagga’—with individual differences observed mostly in snorts, and to a lesser extent in squeals. Analyses based on acoustic features outperformed those based on spectrograms, but each excelled in characterizing different vocalization types. We thus recommend the combined use of these two approaches. This study offers valuable insights into plains zebra vocalization, with implications for future comprehensive explorations in animal communication.
Experimental evidence supports the ability of spotted lanternfly to hitchhike on vehicle exteriors as a mechanism for anthropogenic dispersal
Authors: Elsensohn Johanna E. , Wolford Scott , Tabb Amy , Leskey Tracy
Published: July 2024

Historically, anecdotal observations support the likelihood of human-assisted invasive insect dispersal to new environments. No previous studies have investigated the ability of insects to remain attached to moving vehicles; however, such information is critical for prioritizing research, mitigation activities and understanding anthropogenic effects on biotic communities.Lycorma delicatula(White), spotted lanternfly (SLF), an invasive insect whose range is currently expanding throughout the United States, is commonly observed in urban settings and near transportation hubs. We developed a novel method to test SLF’s ability to remain on vehicle surfaces including bonnet, nose wing, windscreen, wipers and scuttle panel using laminar wind flow from 0 to 100 ± 5 km h−1. We found all mobile life stages (nymphs and adults) could remain on the vehicle up to 100 km h−1. First instar nymphs and early season adults remained attached at significantly higher wind speeds than other stages. A brief acclimatization period prior to wind delivery increased attachment duration for all life stages except later season adults. The importance of outliers in the success of invasive species is well established. Given these results, any hitchhiking SLF could potentially establish incipient populations. This methodology will be beneficial for exploring human-assisted dispersal of other invasive arthropods.
Early agriculture and crop transitions at Kakapel Rockshelter in the Lake Victoria region of eastern Africa
Authors: Goldstein Steven T. , Mueller Natalie G. , Janzen Anneke , Ogola Christine , Dal Martello Rita , Fernandes Ricardo , Li Sophia , Iminjili Victor , Juengst Sara , Odera Otwani Anthony , Sawchuk Elizabeth A. , Wang Ke , Ndiema Emmanuel , Boivin Nicole
Published: July 2024

The histories of African crops remain poorly understood despite their contemporary importance. Integration of crops from western, eastern and northern Africa probably first occurred in the Great Lakes Region of eastern Africa; however, little is known about when and how these agricultural systems coalesced. This article presents archaeobotanical analyses from an approximately 9000-year archaeological sequence at Kakapel Rockshelter in western Kenya, comprising the largest and most extensively dated archaeobotanical record from the interior of equatorial eastern Africa. Direct radiocarbon dates on carbonized seeds document the presence of the West African crop cowpea (
Vigna unguiculata
(L.) Walp) approximately 2300 years ago, synchronic with the earliest date for domesticated cattle (
Bos taurus
). Peas (
Pisum sativum
L. or
Pisum abyssinicum
A. Braun) and sorghum (
Sorghum bicolor
(L.) Moench) from the northeast and eastern African finger millet (
Eleusine coracana
(L.) Gaertn.) are incorporated later, by at least 1000 years ago. Combined with ancient DNA evidence from Kakapel and the surrounding region, these data support a scenario in which the use of diverse domesticated species in eastern Africa changed over time rather than arriving and being maintained as a single package. Findings highlight the importance of local heterogeneity in shaping the spread of food production in sub-Saharan Africa.
A simple optical flow model explains why certain object viewpoints are special
Authors: Stewart Emma E. M. , Fleming Roland W. , Schütz Alexander C.
Published: July 2024

A core challenge in perception is recognizing objects across the highly variable retinal input that occurs when objects are viewed from different directions (e.g. front versus side views). It has long been known that certain views are of particular importance, but it remains unclear why. We reasoned that characterizing the computations underlying visual comparisons between objects could explain the privileged status of certain qualitatively special views. We measured pose discrimination for a wide range of objects, finding large variations in performance depending on the object and the viewing angle, with front and back views yielding particularly good discrimination. Strikingly, a simple and biologically plausible computational model based on measuring the projected three-dimensional optical flow between views of objects accurately predicted both successes and failures of discrimination performance. This provides a computational account of why certain views have a privileged status.
Predictability of ecological and evolutionary dynamics in a changing world
Authors: Bozzuto Claudio , Ives Anthony R.
Published: July 2024

Ecological and evolutionary predictions are being increasingly employed to inform decision-makers confronted with intensifying pressures on biodiversity. For these efforts to effectively guide conservation actions, knowing the limit of predictability is pivotal. In this study, we provide realistic expectations for the enterprise of predicting changes in ecological and evolutionary observations through time. We begin with an intuitive explanation of predictability (the extent to which predictions are possible) employing an easy-to-use metric, predictive power
PP
(
t
). To illustrate the challenge of forecasting, we then show that among insects, birds, fishes and mammals, (i) 50% of the populations are predictable at most 1 year in advance and (ii) the median 1-year-ahead predictive power corresponds to a prediction
R
2
of only 20%. Predictability is not an immutable property of ecological systems. For example, different harvesting strategies can impact the predictability of exploited populations to varying degrees. Moreover, incorporating explanatory variables, accounting for time trends and considering multivariate time series can enhance predictability. To effectively address the challenge of biodiversity loss, researchers and practitioners must be aware of the information within the available data that can be used for prediction and explore efficient ways to leverage this knowledge for environmental stewardship.
comparison of genetic diversity and phylogenetic structure of 18S gene ofTrichomonas vaginalisin Hainan and Xinjiang provinces
Authors: Liu Jun , Dong Xiaoyang , Wang Daping , Chen Min , Nie Jing , Xiao Man
Published: July 2024

Trichomonas vaginalisis a kind of flagellate parasite endemic all of the world. study compared the difference of genetic diversity and phylogenetic structure of 18S ribosomal RNA gene ofT. vaginalisfrom Hainan and Xinjiang Provinces, China. 20 samples and 47 samples from Hainan and Xinjiang respectively which confirmed for infection with T.vaginalis. The sequences were aligned using MEGA 11 software and phylogenetic trees were drawn by Neighbor-Joining method. The number of mutation, nucleotide diversity, and haploid diversity were analyzed using Dnaspv5 software. For Hainan samples, the analyses showed 31 polymorphisms, creat different haplotypes with a haplotype diversity of 0.589. Nucleotide diversity and average nucleotide different amongT.vaginaliswere estimated as 0.00679 and 3.447, respectively.Tajima’s D value in Tajiama’s neutrality test was -2.48147,which was significant (p<0.001). But for Xinjiang samples, the analyses showed 31 polymorphisms, creat different haplotypes with a haplotype diversity of 0.731. Nucleotide diversity and average nucleotide different among T.vaginalis were estimated as 0.00497 and 2.50435, respectively. Tajima’s D value in Tajiama’s neutrality test was -2.26284, which was significant (p<0.01). For all the sequence in this study, all the sequences form one phylogenetic tree, some of the sequence from two provinces showed a certain aggregating phenomenon. The differences between the samples from two province maybe for the local environment, ethnic, sample number and so on, it need further study for T.vaginalis.
The Association between Endometriosis and Immunological diseases
Authors: Shigesi Nina , Harris Holly R. , Fang Hai , Ndungu Anne , Lincoln Matthew R. , Cotsapas Chris , Knight Julian , Missmer Stacey A. , Morris Andrew P. , Becker Christian M. , Rahmioglu Nilufer , Zondervan Krina T. ,   The International Endometriosis Genome Consortium,   The 23andMe Research Team
Published: July 2024

The evidence for a greater prevalence of immunological-diseases among endometriosis patients has varied in robustness and been subject to selection bias. We investigated the phenotypic and genetic association between endometriosis and 31 immunological-diseases in the UK Biobank (8,223 endometriosis, 64,620 immunological-disease cases). In cross-sectional and retrospective cohort analyses, endometriosis patients were at significantly increased (30-80%) risk of classical- autoimmune (rheumatoid arthritis, multiple sclerosis, coeliac disease), autoinflammatory (osteoarthritis) and mixed-pattern (psoriasis) diseases. Osteoarthritis (genetic-correlation (rg)=0.28, P=3.25×10-15), rheumatoid arthritis (rg=0.27, P=1.54×10-5) and multiple sclerosis (rg=0.09, P=4.00×10-3) were significantly genetically correlated with endometriosis. Mendelian randomisation analysis suggested a causal association between endometriosis and rheumatoid arthritis (OR=1.16, 95%CI=1.02-1.33). Expression QTL analyses highlighted effector genes enriched for seven pathways across all four conditions, with three genetic loci shared between endometriosis and osteoarthritis and one with rheumatoid arthritis. Although the increased risk of immunological-diseases among endometriosis patients is modest, their shared genetic basis opens-up opportunities for new treatments.
The Evolving Landscape of Substance Use Disorder Mortality in the United States: A Spatiotemporal Analysis of Emerging Hotspots and Vulnerable Populations (2005-2020)
Authors: Escobar Santiago , MacKinon Neil J. , Ambade Preshit , Hoffman Zach , Cuadros Diego F
Published: July 2024

The escalating Substance Use Disorder (SUD) crisis in the U.S., marked by a significant rise in mortality since 1999, underscores the urgent need for a comprehensive analysis of its spatiotemporal dynamics. This study aims to elucidate the heterogeneous geospatial distribution of SUD mortality, identifying specific locations where vulnerable communities face heightened risk. By examining SUD mortality data from the CDC for the period 2005-2020, we applied scan statistics to delineate temporal and geospatial clusters of elevated SUD-related deaths, further dissecting these patterns across racial subpopulations and regions. Our findings reveal 27 distinct clusters nation-wide, predominantly emerging post-2013 and persisting until 2020, indicating a shifting epicenter of the epidemic. Notably, the white subpopulation was associated with 26 clusters, closely mirroring the broader national trends, yet with a pronounced concentration in the eastern U.S. Conversely, the black subpopulation demonstrated a different pattern, with 17 clusters arising between 2013 and 2020, primarily post-2015, suggesting a temporal and spatial divergence in the impact of the epidemic across racial subpopulations. This analysis not only highlights the critical need for targeted public health interventions and policies but also calls for continued surveillance to monitor and mitigate the evolving SUD crisis. By understanding the complex spatiotemporal and racial variations in SUD mortality, we can better allocate resources, develop effective prevention strategies, and support the communities most in need.
Subsurface Microbial Colonization at Mineral-Filled Veins in 2-Billion-Year-Old Igneous Rock from the Bushveld Complex, South Africa
Authors: Suzuki Yohey , Webb Susan J. , Kouduka Mariko , Kobayashi Hanae , Castillo Julio H. , Kallmeyer Jens , Moganedi Kgabo , Allwright Amy J. , Klemd Reiner , Roelofse Frederick , Mapiloko Mabatho , Hill Stuart J. , Ashwal Lewis D. , Trumbull Robert B.
Published: July 2024

Recent advances in subsurface microbiology have demonstrated the habitability of multi-million-year-old igneous rocks, despite the scarce energy supply from rockwater interactions. Given the minimal evolution coupled with exceedingly slow metabolic rates in subsurface ecosystems, spatiotemporally stable igneous rocks can sustain microbes over geological time scales. This study investigated 2-billion-year-old igneous rock in the Bushveld Complex, South Africa, where ultradeep drilling is being executed by the International Continental Scientific Drilling Program (ICDP). New procedures were successfully developed to simultaneously detect indigenous and contaminant microbial cells in a drill core sample. Precision rock sectioning coupled with infrared, fluorescence and electron microscopy imaging of the rock section with submicron resolution revealed microbial colonization in veins filled with smectite. The entry and exit of microbial cells in the veins are severely limited by tight packing with smectite, the formation of which supplies energy sources for long-term habitability. Further microbiological characterization of drilled rock cores from the Bushveld Complex will expand the understanding of microbial evolution in deep igneous rocks over 2 billion years.
Genetic architecture of the tomato fruit lipidome; new insights link lipid and volatile compounds
Authors: Kuhalskaya Anastasiya , Li Xiang , Lee Jeongah , Gonda Itay , von Steimker Julia , Bulut Mustafa , Karakas Esra , Fisher Josef , Krämer Konrad , Vanholme Ruben , Rosental Leah , Ahchige Micha Wijesingha , Garbowicz Karolina , Klemmer Annabella , Ruß Anne-Kathrin , Donath Andreas , Cuadros-Inostroza Alvaro , Boerjan Wout , Tieman Denise , Zamir Dani , Klee Harry , Alseekh Saleh
Published: July 2024

Tomato (Solanum lycopersicum L.) fruit flavor is determined by a combination of multiple volatile compounds, including several derived from lipids and fatty acids. Although fruit flavor has been intensively studied, the linkage between lipid metabolism and flavor remains largely undefined. Here, we performed a genome-wide association study (GWAS) and QTL mapping for the fruit lipid content from 550 tomato accessions and 107 backcross inbred lines (BILs) in two consecutive seasons. Over 130 lipid compounds were identified and mapped, allowing for the identification of over 600 metabolic QTL (mQTL). We further described and validated candidate genes associated with lipid content. Among them is a lipase-like protein (TomLLP) whose function was validatedin vivousing overexpression lines in tomato and knockout mutants in Arabidopsis. We also identified functions for three enzymes: a class III lipase (Sl-LIP8), a cyclopropane-fatty-acyl-phospholipid synthase (CFAPS1), and Lipoxygenase C (TomLoxC). By utilizing knockout lines forCFAPS1and CRISPR-Cas9 loss-of-function lines forSl-LIP8andTomLoxC, we demonstrated the functional importance of these enzymes in fruit lipid metabolism. Our study provides a comprehensive analysis of the tomato fruit lipidome and insights into key genes that shaped the natural variation in tomato lipid content and their links to flavor-associated volatile compounds.