bluuebunny/crossref_metadata_2025 huggingface dataset:
Placental Infections
Authors: Khullar Poonam , Hon Jane Date , Sethi Shalini , Kim Julia , Iqbal Momin , Chavez Martin R.
Published: December 2024

This comprehensive review examines the effects of various infections on pregnancy, focusing on maternal symptoms, fetal outcomes, diagnostic methods, and placental pathology. The paper covers bacterial, viral, and parasitic infections, their mechanisms of transmission, clinical presentations, and histopathologic findings in the placenta. It emphasizes the importance of early detection and intervention, highlighting the challenges in diagnosis due to often asymptomatic presentations. The review also discusses the placenta’s role as a protective barrier and its immune defense mechanisms against pathogens. Overall, this paper serves as a comprehensive resource for understanding the complex interplay between maternal infections, placental pathology, and fetal outcomes.
Epiretinal Membrane and Senile Cataract: Combined vs Sequential Surgery
Authors: Mori Tommaso , Barone Vincenzo , Nunziata Sebastiano , Surico Pier Luigi , Stefanini Simone , Mastrofilippo Valentina , Di Zazzo Antonio , Coassin Marco
Published: December 2024

Purpose:

To evaluate the outcomes of combined phacovitrectomy versus sequential phacoemulsification and vitrectomy in patients with both senile cataract and epiretinal membrane (ERM).

Methods:

A retrospective multicenter study was conducted between 2014 and 2022 at two hospitals in Italy. Patients with idiopathic ERM and senile cataract in the same eye were enrolled and underwent either combined (n=38) or sequential surgery (n=38), performed by a single surgeon. Best corrected visual acuity (BCVA) and central macular thickness (CMT) were measured at 1, 3, and 6 months after surgery.

Results:

Both surgical approaches significantly improved BCVA and reduced CMT after 6 months. However, sequential surgery showed faster visual recovery, with significant improvements in BCVA (P=0.008) and CMT (P<0.0001) observed as early as 1-month post-surgery, compared to the combined group.

Conclusion:

Although both surgical approaches yielded significant improvements in visual acuity and central macular thickness at 6 months, the sequential approach offered a faster recovery in the early postoperative period. According to the literature, the sequential approach also allows some patients to be satisfied after cataract surgery alone, potentially avoiding unnecessary vitrectomy and reducing the risk of overtreatment.
Factors Associated with Lamina Cribrosa Microvasculature Determined via Swept-Source Optical Coherence Tomography Angiography
Authors: Yoon Jooyoung , Sung Kyung Rim , Lee Jin Yeong , Shin Joong Won , Kim Joon Mo
Published: December 2024

Précis

The lamina cribrosa microvasculature reduction was associated with the posterior deformation of lamina cribrosa, as well as the functional deterioration, in all spectrums of open-angle glaucoma.

Purpose:

To investigate the factors associated with the lamina cribrosa vessel density (LCVD) determined via swept-source optical coherence tomography angiography (SS-OCTA).

Materials and Methods:

The optic nerve head (ONH) scan was obtained using SS-OCTA (PLEX Elite 9000; Carl Zeiss Meditec, Inc., Dublin, CA, USA). The lamina cribrosa curvature index (LCCI) was assessed using seven horizontal B-scan images across the ONH. The LCVD was calculated from the segmented layer at the level of lamina cribrosa (LC). Primary open angle glaucoma (POAG) eyes were categorized into two groups according to the visual field mean deviation (VF MD) (mild to moderate [≥ -12 dB] and advanced [< -12 dB]). The factors associated with the LCVD were evaluated using linear regression analysis.

Results:

A total of 127 POAG and 43 healthy eyes were included. POAG eyes showed significantly thinner circumpapillary retinal nerve fiber layer (cpRNFL) and macular ganglion cell inner plexiform layer (mGCIPL), lower LCVD, and greater LCCI compared to healthy eyes (all P<0.05). In the mild to moderate group, lower LCVD was associated with worse VF MD, thinner cpRNFL and mGCIPL, and greater LCCI (all P<0.05). In the advanced group, the LCVD was associated with VF MD and LCCI (both P<0.05). A greater LCVD was correlated with a greater LCCI in the healthy group (P =0.045).

Conclusions:

Reduced LCVD was associated with an increased LCCI in all spectrums of POAG. LC deformation may affect the ONH microvasculature in glaucoma.
Prevalence of Stress and Burnout in Physical Therapist Clinical Instructors
Authors: Pontiff Ryan J. , Gleeson Peggy , Mitchell Katy , Patel Rupal M.
Published: December 2024

Introduction.

This study investigates the prevalence of stress and burnout among Physical Therapy Clinical Instructors (PT CIs) using the Perceived Stress Scale – 10 (PSS-10) and Oldenburg Burnout Inventory (OLBI) surveys. Given the critical role of PT CIs in student education, understanding their stress and burnout levels is essential.

Review of Literature.

The, PSS-10, a 10-item self-report survey, measures perceived stress with scores ranging from 0 to 40. It has demonstrated good psychometric properties, including test–retest reliability (r = 0.77) and criterion validity (r = −0.70 with short form-36). The OLBI, a 16-item survey, assesses burnout through disengagement and exhaustion subscales, showing strong reliability (r = 0.85) and validity.

Subjects.

The study included 494 PT CIs who met the inclusion criteria of having supervised a student physical therapist within the past 12 months and working full time. Participants were nationally recruited via emails and social media.

Methods.

A cross-sectional design was employed. Participants completed an electronic survey consisting of a demographic form and the PSS-10 and OLBI measures. Data were analyzed using IBM SPSS Statistics, with one-way ANOVAs conducted to assess differences between demographic groups. This study was conducted midway through the COVID-19 pandemic.

Results.

The mean PSS-10 score was 15, indicating moderate stress for 56.1% of participants. The mean OLBI score was 36.95, indicating moderate burnout for 65.4% of participants. Significant differences between groups in both stress and burnout were found across age and marital status variables. Notably, women reported higher burnout levels than men.

Discussion and Conclusion.

Physical Therapy Clinical Instructors exhibit moderate stress and burnout levels, similar to general PT populations. The findings highlight the need for targeted interventions supporting PT CIs, particularly considering the COVID-19 pandemic impact. Future research should explore additional factors influencing PT CI stress and burnout and develop strategies of mitigation.
The role of pharmacogenomic testing in optimizing depression treatment in medically underserved communities: Implications for nurse practitioner practice
Authors: Garcia Gryan
Published: December 2024

Depression is a leading cause of disability worldwide, with treatment-resistant depression (TRD) affecting approximately 30% of patients who do not respond to standard antidepressants. In underserved and uninsured communities, where Nurse Practitioners (NPs) often provide essential mental health care, the challenges of managing TRD are compounded by limited access to specialized services. Pharmacogenomic testing offers a promising approach to overcoming these barriers by providing personalized medication recommendations based on a patient's genetic profile. This brief report examines the medical records of 46 patients from underserved communities who underwent genetic testing for TRD. Of the patients reviewed, 31 achieved remission within 2 months of receiving genetically guided treatment, resulting in a remission rate of 67.39%. Patients with specific genetic markers, such as poor metabolizers for CYP2D6 or CYP2C19, experienced the most significant benefits. These findings suggest that pharmacogenomic testing can significantly improve treatment outcomes for TRD in underserved populations, enabling NPs to provide more personalized, effective care. Further research is necessary to explore the long-term benefits and cost-effectiveness of integrating pharmacogenomic testing into NP-led practices, particularly in resource-limited settings.
Left Ventricular Unloading With Surgically Implanted Microaxial Flow Pump in Patients on Venoarterial Membrane Oxygenation
Authors: Lanmüller Pia , Hinrichs Nils , Nersesian Gaik , Lewin Daniel , O’Brien Ben , Falk Volkmar , Potapov Evgenij , Starck Christoph , Ott Sascha
Published: December 2024

Venoarterial extracorporeal membrane oxygenation (VA-ECMO) is applied for the treatment of cardiogenic shock. Concomitant left ventricular unloading (LVU) with a microaxial flow pump (mAFP) enables myocardial and pulmonary recovery and may overcome some of the limitations of VA-ECMO. The study included 145 cardiogenic shock patients, 89 (61.4%) of whom were treated with VA-ECMO alone (ECMO group), whereas 56 (38.6%) received LVU with a surgically implanted mAFP on top of VA-ECMO (ECMELLA group). After 2:1 propensity score matching, 30 day and 1 year survival was similar between the groups (p = 0.62 and 0.68, respectively). In the subgroup analysis, patients who received mAFP in the first 2 hours after VA-ECMO implantation had an improved 30 day (hazard ratio [HR]: 0.45 [95% confidence interval {CI}: 0.23–0.88], p = 0.02) and 1 year survival (HR: 0.52 [95% CI: 0.28–0.97], p = 0.04). The rate of limb ischemia, hemorrhage, and renal replacement therapy were comparable between the propensity score-matched cohorts. Early LVU with a surgically implanted mAFP in patients on VA-ECMO improved short-and long-term survival.
GLP-1RA based therapies in the young and old
Authors: Rigas Georgia , Alexander Shirley , Haywood Cilla J.
Published: December 2024

Purpose of review

Obesity is recognized as a “gateway” chronic, progressive disease of dysfunctional adipocytes. Glucagon-like peptide-1 receptor agonist-based therapies (GLP1BTs), including glucagon-like peptide-1 receptor agonists (GLP-1 RAs) with/without glucose-dependent insulinotropic polypeptide (GIP), have demonstrated clinically significant weight loss and health gains in adults, hence interest in using them in younger and older people. Therefore, reviewing the role of GLP1BTs in these populations is pertinent and timely.

Recent findings

Recent American Pediatric Guidelines emphasize the need for early introduction of obesity-management medication (OMM). This review evaluates the recently published data evaluating use of GLP1BTs in young people with obesity and/or youth onset Type 2 diabetes (YOT2D).

Large studies of GLP1BTs in adults included those over 65, however no separate trial has looked at this heterogeneous group. This review translates the evidence, as it pertains to those over 65 where possible.

Newer-generation GLP1BTs specifically target pathways involved in energy balance, glycaemic control and other metabolic functions, heralding a new era for the management of younger people.

Published cardiovascular outcome trial (CVOT) data presented in this review support the utility of GLP1BTs in the management of older people living with obesity and/or Type 2 diabetes (T2D), with the reassurance of no new safety signals identified. Maturation of the longer-term data and publication of the additional CVOT data in cohorts of differing health complexity will provide further insights.
Physical activity promotes well-being: medical students’ engagement and perspective. A cross-sectional study scoped through innovation and technology
Authors: Mohamed Sami , Muhammad Surajo Abdulqadir , Mohamed Abdikarim Abdi , Esam Eldeen Ahmad Al-Mujtaba , Alhaj Ahmad Mahmud , Bulama Ahmad Abdullahi
Published: December 2024

Background:

The role of physical activity (PA) in health promotion is further complimented by its disease preventive value. Future doctors’ involvement and advocacy in diverse aspects of such significant role is still under evaluation.

Objectives:

This study aimed to assess medical students’ overall PA engagement and their perspective, and to identify whether their level of engagement affects their advocacy and promotion, while discussing related educational innovations and technological advances.

Methods:

Through a cross-sectional observational study design, stratified sampling from third-, fourth-, and fifth-year medical students attending Nile University, Sudan, during the period from February to April 2020, were included. Descriptive data analysis was done using the SPSS software, and presented including, frequencies, cross-tabulation, Chi-square testing with 95% confidence level, and a P value, after data collection via a structured questionnaire adopting parts of the IPAQ. Study has been reported in line with the STROCSS criteria.

Results:

Out of 188 students, 43% males and 57% females, less than half (91, 48.40%) participated in planned PA, and majority (156, 82.98%) agreed with its health-related significance. Few (57, 30.32%) considered academic load as a barrier, and only 20 (10.60%) were not actively promoting PA engagement to others. Most PA participants were males (57.14%), leaning toward group-based activity (54, 59.34%), making regular plans (51, 56.04%) and motivated by self-health promotion (86, 94.51%) (P < 0.05). Despite majority of students (82.98%) agreement on PA’s benefits, nearly half (51.60%) do not engage, Similarly, overall advocacy for PA promotion in relation to specific people was not statistically significant (P = 0.21). Embedding PA into undergraduate curriculum, use of PA report cards, exercise prescription training and targeted mentoring, in addition to digital bracelets, smart phone applications and internet-based social media, had positive impact on PA participation and promotion.

Conclusion:

Medical students’ understanding of PA health related significance did not equate to increase engagement, despite active promotion. Curricular integration of PA should accompany recent innovative educational strategies to increase their participation and advocation. Future studies are needed to evaluate the role of technology-based and AI-driven PA in achieving this goal.
Relationship of stump length with muscle strength, proprioception, and balance in patients with traumatic unilateral transfemoral amputation
Authors: Kılınç Kamacı Gizem , Örücü Atar Merve , Özcan Fatma , Demir Yasin , Aydemir Koray
Published: December 2024

Background:

Many factors affect the rehabilitation of lower limb amputation. One of these factors is the length of the stump.

Objective:

The aim of this study was to assess the relationship of stump length with muscle strength, proprioception, and balance in patients with traumatic unilateral transfemoral amputation.

Study Design:

Sixteen patients with traumatic unilateral transfemoral amputation were included in this cross-sectional study.

Methods:

Stump length was determined by measuring the distance from the trochanter major to the tip of the stump. Hip extensor and flexor muscle strength on the amputated side was determined using the computer-assisted isokinetic system. The proprioceptive sensation of the lower extremities was measured at hip flexion with computer-assisted isokinetic system. Balance of the patients was determined using the Berg Balance Scale.

Results:

There was a statistically significant negative correlation between the stump length and proprioception measurements (r = −0.508, p = 0.044). There was also a statistically significant correlation between Berg Balance Scale and the flexion total work value at 60° angular velocity (r = 0.541, p = 0.03). There was no significant correlation between stump length and other muscle strength, proprioception, and balance parameters.

Conclusions:

A relationship was found between stump length and proprioception, and balance and hip flexor muscle strength in patients with traumatic unilateral transfemoral amputation. In elective lower limb amputations, the level of amputation should be determined at the most functional level with the longest possible stump.
Hemophagocytic lymphohistiocytosis in HIV-associated HHV8-positive multicentric castleman disease
Authors: Migaud Pascal , Pria Alessia Dalla , Hosmann Kai , Kellerher Peter , Fulgenzi Claudia Anna Maria , Stocker Hartmut , Bower Mark
Published: December 2024

Objective:

The clinical and laboratory characteristics of HHV8-associated Multicentric Castleman Disease (MCD) in people living with HIV (PLWH) overlap with those of Hemophagocytic Lymphohistiocytosis (HLH) disease and indeed the two diagnoses may co-exist. A risk-stratified treatment approach to MCD based on Rituximab immunotherapy for mild cases and chemo-immunotherapy for severe cases has been shown to yield excellent outcomes in PLWH. In contrast, HLH disease, previously known as secondary HLH, has a dismal prognosis even when promptly treated according to guidelines.

Design:

A retrospective multicentre cohort study.

Methods:

Retrospective analysis of prospectively collected clinical and pathological data on patients with biopsy proven HIV-associated MCD at the National Centre for HIV Malignancy at Chelsea and Westminster Hospital, London between 2008 and 2024 and at the Department of Infectious Diseases at St. Joseph Hospital Berlin-Tempelhof, Germany between 2020 and 2024.

Results:

In our UK-German cohort including 113 PWLH with MCD, we confirmed that HLH disease secondary to MCD is common (30%) and we demonstrated that HLH disease in this context does not adversely influence survival or risk of MCD relapse.

Conclusion:

We suggest that a high HScore in MCD should not lead to a change in the treatment in this specific setting.
Correlations Between the Pterygomaxillary Junction and Appropriate Osteotome Placement Angles During Junction Separation in Le Fort I Osteotomy
Authors: Limthanakul Isara , Chen Gloria , Chuang Kai-Ti , Chou Pang-Yun , Chen Yu-Ray
Published: December 2024

Purpose:

The authors evaluated pterygomaxillary junction angles across malocclusion patterns and identified the optimal technique for effective pterygomaxillary junction separation during Le Fort I osteotomy, focusing on appropriate osteotome angles and clinical applications.

Methods:

This retrospective study included 211 patients with malocclusion who had undergone Le Fort I osteotomy at Chang Gung Craniofacial Center between December 2015 and September 2023. The patients were stratified by sex and malocclusion class (class I, II, or III). Preoperative cone-beam computed tomography was performed to measure pterygomaxillary junction angles at 2 axial levels: the posterior nasal spine level and the lower border level corresponding to the maxillary tuberosity. Le Fort I osteotomy involving an angle oscillating saw, and a curved-tip Dautrey osteotome was performed, ensuring the precise placement of the osteotome and tilting of the osteotome handle during pterygomaxillary junction separation. The correlations between the pterygomaxillary junction and appropriate osteotome placement angles were investigated.

Results:

Among the 211 patients, 5%, 15%, and 80% had class I, class II, and class III malocclusion, respectively. At the posterior nasal spine level, the average angles of the pterygomaxillary junction relative to the coronal plane were 16.76, 19.16, and 17.82 degrees in class I, class II, and class III groups, respectively; the corresponding angles at the lower border level were 27.29, 27.80, and 25.91 degrees. No significant between-class or between-sex differences were observed in pterygomaxillary junction angles; however, significant differences were noted between the 2 levels.

Conclusion:

Our surgical technique was both safe and effective for pterygomaxillary junction separation.
The effects of listening on speaker and listener while talking about character strengths: an open science school-wide collaboration
Authors: Moin Tia , Weinstein Netta , Itzchakov Guy , Branson Amanda , Law Beth , Yee Lydia , Pape Emma , Cheung Rebecca Y. M. , Haffey Anthony , Chakrabarti Bhismadev , Beaman Philip
Published: December 2024

Listening is understood to be a foundational element in practices that rely on effective conversations, but there is a gap in our understanding of what the effects of high-quality listening are on both the speaker and listener. This registered report addressed this gap by training one group of participants to listen well as speakers discuss their character strengths, allowing us to isolate the role relational listening plays in strengths-based conversations. Participants were paired and randomly assigned to a high-quality listening (experimental) or moderate-quality listening (comparison) condition manipulated through a validated video-based training. High-quality listening predicted a more constructive relational experience; specifically, positivity resonance. Intrapersonal experiences (perceived authenticity and state anxiety) were not affected. Those who engaged in high-quality listening expressed a behavioural intention to continue listening, but condition did not predict a behavioural intention for speakers to continue applying character strengths. This is the first evidence of positivity resonance as a shared outcome between both a speaker and listener when the listener conveys high-quality (as opposed to ‘everyday’) listening. These early findings merit further study with stronger listening manipulations to explore the potential role of listening within interpersonal communication, and inform the applied psychological sciences (counselling, psychotherapy, coaching, organizational, education).
Increasing environmental fluctuations can dampen variability of endogenously cycling populations
Authors: Kortessis Nicholas , Ponciano José Miguel , Simon Franz W. , Ferguson Jake M.
Published: December 2024

Understanding how populations respond to increasingly variable conditions is a major objective for natural resource managers forecasting extinction risk. The lesson from current modelling is clear: increasing environmental variability increases population abundance variability. We show that this paradigm fails to describe a broad class of empirically observed dynamics, namely endogenously driven population cycles. In contrast to the dominant paradigm, these populations can exhibit reduced long-run population variance under increasing environmental variability. We provide evidence for a mechanistic explanation of this phenomenon that relies on how stochasticity interacts with long transient dynamics present in the deterministic cycling model. This interaction stands in contrast to the often assumed additivity of stochastic and deterministic drivers of population fluctuations. We show evidence for the phenomenon in two cyclical populations: flour beetles and Canadian lynx. We quantify the impact of the phenomenon with new theory that partitions the effects of nonlinear dynamics and stochastic variation on dynamical systems. In both empirical examples, the partitioning shows that the interaction between deterministic and stochastic dynamics reduces the variance in population size. Our results highlight that previous predictions about extinction under environmental variability may prove inadequate to understand the effects of climate change in some populations.
Diffusion-induced elastic cavitation
Authors: De Pascalis Riccardo
Published: December 2024

The diffusion of atoms in deformable materials induces volumetric changes through inhomogeneous deformations. We show that when a radially charging solute concentration diffuses within an incompressible, homogeneous, isotropic elastic spherical particle, it can generate stress capable of opening a cavity in its interior without requiring any external load. We investigate for critical threshold by associating the particle with chemo and neo-Hookean elastic potentials. Furthermore, we analyse a pre-existing cavity and study its expansion in the most general case of Mooney–Rivlin elastic potential, determining the deformation and stress fields.
Exploring immune memory traits in the social immunity of a fungus-growing ant
Authors: Goes Aryel C. , Kooij Pepijn W. , Haifig Ives , Bueno Odair C. , Rodrigues Andre
Published: December 2024

The immune system is crucial for organisms to defend against pathogens. Likewise, analogous immune features evolved against similar pressures at the superorganism scale. Upregulating hygiene to the same fungus pathogen is one assumption for convergent immune mechanisms in social insects, although more evidence of immune memory features remains to be confirmed. Here, we assess immune memory traits at the colony level in the leaf-cutting ant
Atta sexdens
. We exposed their fungus cultivar to both homologous and heterologous challenges with the entomopathogenic fungi
Metarhizium anisopliae
and
Beauveria bassiana
, as well as the mycoantagonistic fungi
Fusarium oxysporum
and
Trichoderma spirale
. By measuring ants’ behaviours, we evaluated the capacity of
A. sexdens
: (i) to enhance their collective hygiene, (ii) speed their hygiene in further infections, (iii) how long this capacity lasts in the colonies and (iv) the degree of specificity to increase hygienic responses. Fungus grooming behaviour was enhanced mostly against entomopathogenic fungi, with a trend of faster reactions during homologous challenges. In general, the capacity to elicit such upregulated actions lasted for up to 30 days, but no longer than 60 days. Overall, colonies exhibited a degree of immune specificity, enhancing hygiene only in response to homologous exposures but decreasing it when infected secondarily with a different fungus, indicating flexible social immunity of
A. sexdens
after immune challenges.
The origin and evolution of shrews (Soricidae, Mammalia)
Authors: Yuan Haobo , Dickson Ephriam D. , Martinez Quentin , Arnold Patrick , Asher Robert J.
Published: December 2024

Shrews are among the most speciose of mammalian clades, but their evolutionary history is poorly understood. Their fossil record is fragmentary and even the anatomy of living groups is not well documented. Here, we incorporate the oldest, most complete fossil shrew yet known into the first phylogenetic analysis of the group to include molecular, morphological and temporal data. Our study reveals previously unknown diversity among total- and crown-group soricids. This includes a novel element of the mammalian skeleton: a robust, needle-like sesamoid extending cranially from the second thoracic neural arch in Myosoricini, comparable in length to these species' humeri. Additionally, ‘red-toothed’ shrews have an unusually elongate basicranium, and ‘white-toothed’ shrews probably evolved from a common ancestor with dental pigmentation. The fossil
Domnina
and crown soricids have a double-jaw articulation and incomplete zygomatic arch, but unlike nearly all crown species,
Domnina
has open vomeronasal canals and a tympanic process of the basisphenoid.
Domnina
and other heterosoricids are phylogenetically outside crown Soricidae. The oldest, well-supported total-group soricoids are North American, not Asian, and Soricidae probably originated during the Palaeocene or early Eocene. The diverse mammalian genus
Crocidura
originated and began to diversify during the Miocene.
Predicting Mental and Neurological Illnesses Based on Cerebellar Normative Features
Authors: Kim Milin , Sharma Nitin , Leonardsen Esten H. , Rutherford Saige , Selbæk Geir , Persson Karin , Steen Nils Eiel , Smeland Olav B. , Ueland Torill , Richard Geneviève , Manoli Aikaterina , Valk Sofie L. , Alnæs Dag , Beckman Christian F. , Marquand Andre F. , Andreassen Ole A. , Westlye Lars T. , Wolfers Thomas , Moberget Torgeir
Published: December 2024

Mental and neurological conditions have been linked to structural brain variations. However, aside from dementia, the value of brain structural characteristics derived from brain scans for prediction is relatively low. One reason for this limitation is the clinical and biological heterogeneity inherent to such conditions. Recent studies have implicated aberrations in the cerebellum – a relatively understudied brain region – in these clinical conditions. Here, we used machine learning to test the value of individual deviations from normative cerebellar development across the lifespan (based on trained data from >27k participants) for prediction of autism spectrum disorder (ASD) (n=317), bipolar disorder (BD) (n=238), schizophrenia (SZ) (n=195), mild cognitive impairment (MCI) (n=122), and Alzheimer’s disease (AD) (n=116). We applied several atlases and derived median, variance, and percentages of extreme deviations within each region of interest. Our results show that lobular and voxel-wise cerebellar data can be used to discriminate healthy controls from ASD and SZ with moderate accuracy (the area under the receiver operating characteristic curves ranged from 0.56 to 0.64), The strongest contributions to these predictive models were from posterior regions of the cerebellum, which are more strongly linked to higher cognitive functions than to motor control.
Identification of Circular RNAs associated with Ageing of the Dorsolateral Prefrontal Cortex across the Adult Lifespan
Authors: Amjadi-Moheb Fatemeh , Gobhidharan Sumangali , Mohan Adith , Sachdev Perminder S. , Thalamuthu Anbupalam , Mather Karen A
Published: December 2024

Background

Circular RNAs (circRNAs) are emerging as crucial regulators of biological processes and have been implicated in age-related diseases. Few studies have explored age-related circRNA expression in the human brain across the adult lifespan. This study aims to identify age-related differentially expressed circRNAs in human post-mortem dorsolateral prefrontal cortex (DLPFC) samples, a region critically involved in cognition that exhibits early signs of age-related changes.

Methods

Total RNA sequencing was conducted on a discovery cohort of 67 postmortem DLPFC samples, from individuals with no neurological disease diagnosis at the time of death (35-103 years). CircRNAs were identified using CIRCexplorer2, with 11,907 circRNAs available for analyses. Linear regression was used to analyse the relationships between circRNA expression and age at death. Replication of the results was performed in an independent neurologically healthy dataset from the CommonMind Consortium (n=321, age at death: 35-91 years). Co-expression network analysis was performed to identify modules of highly co-expressed circRNAs associated with age. Potential microRNA and RNA-binding protein target sites were predicted.

Results

In the discovery dataset, 37 circRNAs were age-associated (FDR <0.05). Seven out of the 37 were successfully replicated. The host genes of replicated age-associated circRNAs are implicated in synapse regulation. Co-expression analysis revealed two circRNA modules significantly correlated with age. We identified 484 microRNA and 99 RNA-binding protein target sites on the replicated circRNAs.

Conclusion

Seven age-associated circRNAs were identified as important candidates for involvement in post-transcriptional regulatory networks in the DLPFC. Future studies should aim to elucidate their functional roles in brain ageing.
scSurv: a deep generative model for single-cell survival analysis
Authors: Mizukoshi Chikara , Kojima Yasuhiro , Hayashi Shuto , Abe Ko , Kasugai Daisuke , Shimamura Teppei
Published: December 2024

Single-cell omics analysis has unveiled the heterogeneity of various cell types within tumors. However, no methodology currently reveals how this heterogeneity influences cancer patient survival at single-cell resolution. Here, we introduce scSurv, combining a Cox proportional hazards model with a deep generative model of single-cell transcriptome, to estimate individual cellular contributions to clinical outcomes. The accuracy of scSurv was validated using both simulated and real datasets. This method identifies cells associated with favorable or adverse prognoses and extracts genes correlated with their contribution levels. In melanoma, scSurv reproduces known prognostic macrophage classifications and facilitates hazard mapping through spatial transcriptomics in renal cell carcinoma. We also identified genes consistently associated with prognosis across multiple cancers and demonstrated the applicability of this method to infectious diseases. scSurv is a novel framework for quantifying the heterogeneity of individual cellular effects on clinical outcomes.
MatriCom: a scRNA-Seq data mining tool to infer ECM-ECM and cell-ECM communication systems
Authors: Lamba Rijuta , Paguntalan Asia M. , Petrov Petar B. , Naba Alexandra , Izzi Valerio
Published: December 2024

The ECM is a complex and dynamic meshwork of proteins that forms the framework of all multicellular organisms. Protein interactions within the ECM are critical to building and remodeling the ECM meshwork, while interactions between ECM proteins and cell surface receptors are essential for the initiation of signal transduction and the orchestration of cellular behaviors. Here, we report the development of MatriCom, a web application (https://matrinet.shinyapps.io/matricom) and a companion R package (https://github.com/Izzilab/MatriCom), devised to mine scRNA-Seq datasets and infer communications between ECM components and between different cell populations and the ECM. To impute interactions from expression data, MatriCom relies on a unique database, MatriComDB, that includes over 25,000 curated interactions involving matrisome components, with data on 80% of the ∼1,000 genes that compose the mammalian matrisome. MatriCom offers the option to query open-access datasets sourced from large sequencing efforts (Tabula Sapiens, The Human Protein Atlas, HuBMAP) or to process user-generated datasets. MatriCom is also tailored to account for the specific rules governing ECM protein interactions and offers options to customize the output through stringency filters. We illustrate the usability of MatriCom with the example of the human kidney matrisome communication network. Last, we demonstrate how the integration of 46 scRNA-Seq datasets led to the identification of both ubiquitous and tissue-specific ECM communication patterns. We envision that MatriCom will become a powerful resource to elucidate the roles of different cell populations in ECM-ECM and cell-ECM interactions and their dysregulations in the context of diseases such as cancer or fibrosis.

ONE SENTENCE SUMMARY

MatriCom is a web application devised to mine scRNA sequencing datasets to infer ECM-ECM and cell-ECM communication systems in the context of the diverse cell populations that constitute any tissue or organ.
Characterization and identification of enzyme-producing microflora isolated from the gut of freshwater Prawn,MacrobrachiumSpp
Authors: Nimbalkar Dhanraj N , Nalavade Virdhaval M. , Chavan Jaykumar J.
Published: December 2024

Isolation of extracellular enzyme degrading aerobic bacteria in the digestive tracts of fresh water prawn was carried out. Gut bacteria were isolated on carboxymethyl cellulose agar plates, starch agar media plates, gelatine peptone agar media plates. The isolated strain was qualitatively screen based on their extracellular enzyme on selective media. The strain was characterised based on morphological, physiological and biochemical characterization identified Bacillus species. Bacillus species was isolated by colony characterization carried out by using Gelatin agar Media, carboxymethyl cellulose media and congo red CMC media and starch agar media for different enzyms. Isolates are capable of hydrolysing proteins and carbohydrates indicating their importance in fish nutrition.
Depletion of aneuploid cells is shaped by cell-to-cell interactions
Authors: Fusari Elena , Muzzopappa Mariana , Gracia Juliette , Milán Marco
Published: December 2024

Aneuploidy, the major cause of miscarriages in humans, is pervasive in early embryos but robustly dampened during development, allowing for healthy births. Later in life, aneuploidy correlates with pathological conditions including cancer. Identification of the mechanisms underlying the elimination of aneuploid cells is relevant in development and disease. Here we generated cells carrying molecularly defined segmental monosomies and trisomies and characterized their immediate impact on cellular behavior. Our data reveal signs of out-competition of cells carrying monosomies in genomic regions devoid of previously known haploinsufficient genes. Dose-dependent effects of single genes or a discrete number of genes contribute to the observed cellular behaviors. By simultaneously inducing cells carrying monosomies and trisomies of the same genomic location, we present evidence that segmental trisomies potentiate or alleviate the negative effects of the monosomy on growth, thus revealing a key role of cell interactions in defining thein vivoelimination of aneuploid cells.

Highlights

Segmental monosomies cause growth impairment and are out-competed.

Growth impairment relies on dose-dependent effects of single genes or a discrete number of genes. Segmental trisomies of up to 1500 genes do not have a major impact on proliferation and survival. Cell competition is modulated by the presence of cells trisomic for the same genomic region.

eTOC Blurb

Aneuploidy has a negative impact on the growth and proliferation of all animal cells analyzed so far. Fusari et al. unravel a role of cell interactions in defining thein vivoelimination of aneuploid cells through cell competition.
CoPPIs Algorithm: A Tool to Unravel Protein Cooperative Strategies in Pathophysiological Conditions
Authors: Lomagno Andrea , Yusuf Ishak , Tosadori Gabriele , Bonanomi Dario , Mauri Pierluigi , Di Silvestre Dario
Published: December 2024

We present here the Co-expressed Protein-Protein Interactions (CoPPIs) algorithm. In addition to minimizing correlation-causality imbalance and contextualizing PPIs to the investigated systems, it combines PPIs and protein co-expression networks to identify differentially correlated functional modules. To test CoPPIs, we processed a set of proteomic profiles from different brain areas of controls and subjects affected by idiopathic Parkinson’s disease or carrying a GBA1 mutation. Its robustness was supported by the extraction of functional modules, related to translation and mitochondria, whose involvement in PD pathogenesis is well documented. Furthermore, the selection of hubs and bottlenecks from the weighted PPI networks provided molecular clues consistent with the PD pathophysiology. Of note, like quantification, the CoPPIs algorithm revealed less variations when comparing disease groups than when comparing diseased and controls. However, correlation and quantification results showed low overlap, suggesting the complementarity of these measures. An observation that opens the way to a new investigation strategy that takes into account not only protein expression, but also the level of coordination among proteins that cooperate to perform a given function.
The evolution of weaponry and aggressive behaviour in field crickets
Authors: Judge Kevin A. , Smith Briana E. , Ohlmann Shawna L. , Steckler Deanna K. , Kellington Alexandria T. , Cade William H.
Published: December 2024

Weapons are among the most extravagant sexually selected traits known, yet the evolution of weapon diversity remains understudied. We used field crickets (Orthoptera, Gryllinae) to test two hypotheses explaining interspecific diversity in weaponry. We raised eight species ofGryllusfield crickets under common garden conditions and staged interactions between conspecific males. We measured body size and weapon shape (relative head and mouthpart size) to determine weapon allometry in both males and females, quantified the intensity of male-male aggression for each species, analyzed the effects of both body size and weapon shape on contest outcome, and tested comparative relationships between morphology and behaviour using phylogenetic least squares regression. We found that larger males won more contests than smaller males in seven of eight species, and weapon shape predicted contest success in only one species. Contrary to the fighting advantage hypothesis, body size was not related to aggressiveness across species, but weaponry was. Additionally, the most aggressive species had the most elaborate weaponry, contrary to the weapon-signal continuum hypothesis. Our results highlight the complexity of weaponry evolution in a group of organisms that has been a model system for the observation and study of aggression for approximately 1000 years.
Exploring Bioelectricity with Ace2N-mNeon during Zebrafish Embryogenesis
Authors: Wu ZhenZhen , Silva Rui Oliveira , Houssein Ruya , Trujillo Fabiola Marques , Gotti Jordan , Ganapathy Srividya , Gao Zhenyu , Brinks Daan
Published: December 2024

Bioelectricity is a fundamental biophysical phenomenon present in all cells, playing a crucial role in embryogenesis by regulating processes such as neuronal signaling, pattern formation, and cancer suppression. Precise monitoring of bioelectric signals and their dynamic changes throughout development is vital for advancing our understanding of higher organisms. However, the lack of suitable techniques for mapping bioelectric signals during early development has greatly limited our ability to interpret these mechanisms. To address this challenge, we developed an Ace2N-mNeon expression library in zebrafish, which exhibits membrane localization from 4 hours post-fertilization to at least 5 days post- fertilization and broad expression across multiple cell types throughout development. We validated the use of this library for studying bioelectric changes via voltage imaging to record signals in neurons and cardiomyocytes at different development stages. Through this approach, we found evidence of synchronized neuronal activity during early embryogenesis and observed faster voltage dynamics in cardiomyocytes as development progressed. Our results show that the Ace2N-mNeon library is a valuable tool for developmental bioelectric studies supporting advanced techniques such as voltage imaging and fluorescence lifetime imaging (FLIM). These methods enable non-invasive, dynamic monitoring of bioelectric signals across diverse cell types throughout development, significantly surpassing the capabilities of current electrophysiological techniques.
Phylogeography and genetic structure of the steppe marmot (Marmota bobakMüller, 1776)
Authors: Brandler Oleg , Tambovtseva Valentina , Tukhbatullin Andrey , Rumyantsev Vadim , Grachov Alexey , Kapustina Svetlana
Published: December 2024

The steppe marmotMarmota bobakis a key species in the steppe ecosystems of Eurasia and an important object of economic and conservation practice. Its wide distribution is separated by many ecological and geographical barriers. The studied morphological variability is characterized by clinal variation of characters and indistinct differences. The subspecies system, including three subspecies, has no clear spatial boundaries and is controversial. The genetic variability ofM. bobakhas not been extensively studied. We first investigated the genetic variability ofM. bobakthroughout its range using three traditional molecular markers of the mitochondrial genomeCOI, cytb, and a control region of mtDNA. We found two phylogroups in the genetic structure of this species, which are geographically arranged in an unexpected way. Also, the character of intraspecific genetic variability does not agree with the accepted subspecies division; individuals from terra typica of all three described subspecies belong to the same phyletic lineage. Further studies are needed to develop the subspecies system ofM. bobak.
A complex adaptive systems model of labor reciprocity and normative reasoning in swidden agriculture
Authors: Tverskoi Denis , Scaggs Shane A. , Downey Sean S.
Published: December 2024

Swidden (aka “slash-and-burn”) agriculture is a prototypical coupled human and natural system and understanding the social, cultural, and environmental factors shaping the trajectories of swidden forests is essential to mitigate climate change and ensure equitable collaboration between scientists, planners, and Indigenous communities. Despite this, mathematical models integrating its social and ecological dynamics are rare. Here, we use complex adaptive systems theory to develop a model where individuals rely on labor exchange driven by reciprocity, and on normative reasoning that can lead to sanctions. Our results identify three emergent regimes: low-intensity swidden, sustainable high-intensity swidden that maximizes ecosystem services and harvest returns, and deforestation. We show that sustainable high-intensity swidden evolves if labor reciprocity and normative reasoning are balanced: helping behavior should be significantly conditioned by normative reasoning to prevent over-harvesting, while reciprocity is necessary to prevent excessive sanctioning. We find that the sustainable high-intensity swidden regime is robust to changes in group size, is resilient to environmental shocks, can evolve under various models of forest ecology, and is most productive for both forests and farmers when the balance of labor reciprocity and normative reasoning results in an intermediate scale of forest disturbance. Overall, we illuminate the importance of Indigenous social norms and customary practices related to swidden labor in maintaining sustainable and intensive swidden agriculture.
Deep Learning-Driven Subtype Classification of Colorectal Cancer Using Histopathology Images for Personalized Medicine
Authors: Le Phan Nghia Trong , Mavuso Mqondisi Fortune , Thien Dao Phuc Nguyen , Anh Nguyen Huy Ngoc , Thuy Mai Tien , Thi Quang Kiep , Le Thang Truong
Published: December 2024

Precise and timely diagnosis of colorectal cancer (CRC) is vital for enhancing patient outcomes. Histopathological examination of tissue samples remains the gold standard for CRC diagnosis, but it is a time-consuming and subjective approach tending to inter-observer variability. This study explores the use of deep learning, particularly ResNet architectures, for the automated classification of CRC using histopathology images. Our research focuses on evaluating different ResNet models (ResNet-18, ResNet-34, ResNet-50) to extract relevant visible characteristics. Additionally, we use Grad-CAM heatmaps to understand the model’s areas of focus, ensuring alignment with established diagnostic criteria. To address limited data availability, we examine data augmentation techniques to improve the model’s adaptability. Our analysis indicates that ResNet-34 strikes a balance between model complexity and performance, demonstrating notable accuracies of 91.10%, 99.11%, and 100.00% for overall, top-2, and top-3 accuracy classifications, respectively, outperforming both shallower (ResNet-18) and deeper (ResNet-50) models. This indicates that a moderate depth is practical in capturing features of CRC images. Our findings have significant importance for the development of an interpretable AI-assisted diagnostic tool for CRC, with the potential to improve the efficiency and accuracy of pathologists. This approach aims to automate image analysis, offer insights into model decisions, and ultimately improve diagnostic consistency and patient care in oncology.