bluuebunny/crossref_metadata_2025 huggingface dataset:
Professionals’ Reported Practices to Involve Families in Initial Evaluations for Early Intervention and Early Childhood Special Education
Authors: Stein Rachel , Steed Elizabeth , Charlifue-Smith Renee
Published: November 2024

It is well recognized and codified into law that families are an important part of early childhood evaluations; how families are included in evaluations in practice is less clear. To learn about family involvement, a nationally distributed survey focused on early childhood professionals’ (n = 1,118) use of family-centered practices before, during, and after the initial evaluation for early intervention (EI) and preschool special education. A mixed methods design was utilized to explore how professionals reported to involve families before, during, and after initial evaluations. Results varied for professionals involved in initial evaluations for EI versus preschool special education. Qualitative analyses revealed the challenges professionals identified when attempting to engage families in the initial evaluation process. Implications of the study findings are discussed for policy, practice, and research related to family involvement in the initial evaluation process.
Optimization of Clozapine Treatment
Authors: Olmos Ismael , Ricciardi Carina , Mato Mauricio , Guevara Natalia , Acuña Sabrina , Maldonado Cecilia , Vázquez Marta , Toledo Mauricio , Menéndez Clara , Blanco Valentina , Badano José L. , Cayota Alfonso , Spangenberg Lucia , Cardenas-Rodriguez Magdalena
Published: November 2024

Purpose/Background

Clozapine is the recommended drug for treatment-resistant schizophrenia. Drug response could be affected by numerous factors such as age, sex, body mass index, co-medication, consumption of xanthine-containing beverages, smoking, and genetic variants of the enzymes involved in clozapine metabolism (CYP1A2, CYP3A4, and, to a lesser extent, CYP2C19 and CYP2D6). This study evaluated genetic and nongenetic variables that may affect clozapine plasma concentrations in Uruguayan patients with schizophrenia.

Methods/Procedures

Demographic data including sex, age, ethnicity, body weight, smoking habit, concomitant medication, and xanthine consumption were collected through a data collection form. Clozapine and norclozapine concentrations were determined using an HPLC system equipped with a UV detector. Genetic variants were determined through next-generation sequencing using Illumina sequencing technology and a panel of DNA probes.

Findings/Results

Fifty patients were included in the study. After evaluation, only tobacco use and obesity had a significant impact on clozapine exposure (P < 0.05). The high prevalence of the genetic variant CYP1A2*1F may account for the significant impact that tobacco smoking has on clozapine concentrations. Some common adverse effects observed in this study depend on clozapine plasma concentrations, such as constipation and sialorrhea.

Implications/Conclusions

These types of studies provide the clinician with tools to optimize clozapine therapy, attempting to use the minimum effective dose and attenuating the burden of concentration-dependent adverse reactions.
Grenfell Tower Fire: Toxic Effluents and Assessment of Firefighters’ Health Impacts
Authors: Stec Anna A. , Purser David A. , Hull T. Richard
Published: November 2024

Objective

This study assesses the health symptoms and longer- term health outcomes of firefighters who attended the Grenfell Tower fire.

Methods

All available data sources were analysed, including databases published by the Public Inquiry, the Firefighter Cancer and Disease Registry, incident logs and sickness reports up to 3 years post-fire.

Results

Over three times as many firefighters who reported exposure to smoke during the fire, also reported digestive and respiratory diseases following the fire, compared to those not reporting exposure to smoke. Other, more complex relationships are reported between smoke exposure, immediate health symptoms and longer-term health outcomes.

Conclusions

The incident’s urgency led professional firefighters to operate without respiratory protection equipment resulting in debilitating health effects.
The Relationship Between the Electrically Evoked Stapedius Reflex Threshold and Stimulus Burst Duration in Pediatric Cochlear Implant Users: Preliminary Data
Authors: Walkowiak Adam , Kontides Alejandra , Takanen Marko , Obrycka Anita , Skarżyński Piotr , Skarżyński Henryk , Lorens Artur
Published: November 2024

Introduction

The electrically evoked stapedius reflex threshold (eSRT) is an objective measure that helps to fit cochlear implants (CIs). The primary aim of this study was to investigate the relationship between different burst durations to elicit eSRT in pediatric CI users.

Materials and Methods

Different stimuli burst durations (100–500 ms) were applied to observe the effect in the reflex determination in 11 pediatric CI users. Reflexes were measured in electrode contacts #2, #6, #9, and #11. Testing was conducted at 9 months after CI activation.

Results

Burst duration and electrode contact site both had a significant effect on eSRT (p < 0.001). The lowest eSRT thresholds were obtained with the longest burst duration. The highest stimulation level was required to elicit a reflex at basal electrode contacts. No significant effect was found for the interaction between electrode contact site and burst duration.

Discussion

Burst durations of 100 ms yielded significantly larger eSRT thresholds than 300- and 500-ms burst durations. Thresholds obtained with the longest (i.e., traditional) burst durations reflected maximum comfortable loudness (MCL) levels typically found at early post-activation stages. In contrast, 100-ms burst yielded threshold levels similar to MCLs that have stabilized. We therefore consider both short (100 ms) and longer (300 or 500 ms) bursts useful in the clinical practice.

Conclusion

The best burst duration to use depends on the interval: longer burst durations are useful for estimating MCLs for earlier intervals, whereas shorter burst durations are useful for later intervals. These findings may help clinicians optimize fittings in cases where using behavioral responses is problematic.
Medicaid Policy and Hepatitis C Treatment Among Rural People Who Use Drugs
Authors: Stopka Thomas J. , Whitney Bridget M. , de Gijsel David , Brook Daniel L. , Friedmann Peter D. , Taylor Lynn E. , Feinberg Judith , Young April M. , Evon Donna M. , Herink Megan , Westergaard Ryan , Koepke Ruth , Havens Jennifer R. , Zule William A. , Delaney Joseph A. , Pho Mai T.
Published: November 2024

Background:

Restrictive Medicaid policies regarding hepatitis C virus (HCV) treatment may exacerbate rural health care disparities for people who use drugs (PWUD). We assessed associations between Medicaid restrictions and HCV treatment among rural PWUD.

Methods:

We compiled state-specific Medicaid treatment policies across 8 US rural sites in 10 states and merged these with participant survey data. We hypothesized that local restrictions regarding prescriber type, sobriety, and fibrosis estimates were associated with HCV treatment outcomes. We conducted a cross-sectional, ecological analysis of treatment restrictions and HCV treatment outcomes using bivariate analyses to characterize differences between PWUD who initiated HCV treatment and unadjusted logistic regressions to assess associations between restrictions and treatment.

Results:

Among 944 participants, 111 (12%) reported receiving HCV treatment. Participants receiving treatment were older [median age (interquartile range): 42 (34–53) vs. 35 (29–42), P<0.001], more likely to receive disability support (32% vs. 20%, P=0.002), and less likely to be Medicaid-insured (57% vs. 71%, P < 0.001). More PWUD in states without any restrictions reported receiving treatment (17% vs. 11%, P=0.08) and achieving HCV cure/clearance (42% vs. 30%, P=0.01) than in states with restrictions. Restrictions were associated with lower odds of receiving HCV treatment (odds ratio=0.61, 95% CI: 0.35–1.06, P=0.08). Sensitivity analyses showed a similar association with HCV cure/clearance (odds ratio=0.60, 95% CI: 0.40–0.91, P=0.02).

Conclusions:

We identified significant unadjusted associations between Medicaid restrictions and receipt of HCV treatment and cure, which has substantial implications for health outcomes among rural PWUD. Lifting remaining Medicaid restrictions will be critical to achieving HCV elimination.
Spontaneous recovery of active shoulder external rotation in patients with brachial plexus birth injury
Authors: Hyttinen Maria , Rönkkö Henrikki , Paavilainen Pasi , Helminen Mika , Jokihaara Jarkko
Published: November 2024

Background:

Brachial plexus birth injuries (BPBI) occur as a result of a difficult delivery. External rotation of shoulder (ER) is usually one of the last movements which may recover. There is no consensus about the predicting factors for spontaneous recovery or the optimal timing for surgical treatment of ER in BPBI patients. The aim of our retrospective study was to describe spontaneous recovery of active ER and evaluate predicting factors for the recovery.

Methods:

We screened 562 patients and identified a consecutive cohort of 103 BPBI patients, who had no active ER at the age of 3 months. We systematically collected clinical data on recovery. In addition, we assessed whether early recovery of elbow flexion, shoulder abduction or Narakas grade at 1 month predicts ER recovery.

Results:

Fifty-two (51%) patients spontaneously recovered ER, 44% of whom were recovered by the age of 1 year, 83% by 1.5 years, 92% by 2 years and 98% by 3 years. A breakpoint in the slope of the curve showing proportion of recovered patients occurred at 2 years of age. Recovery of active ER was significantly associated with early elbow flexion and Narakas grade at 1 month, but not with early active shoulder abduction.

Conclusions:

Most spontaneous recovery of ER in patients with BPBI occurs until 2 years of age, which thus can be considered a meaningful follow-up period for spontaneous recovery of ER. This information should be considered when making decision about peripheral nerve transfer surgery to improve ER in BPBI.
Evidence of 18F-FDG Utility in Rare Case of Metastatic Anal Melanoma With Prolonged Survival
Authors: Ranes Jennifer Marie Catherine , Ormaza Vera Ana Jamileth , Flynt Lesley
Published: November 2024

A 43-year-old woman presented with an anorectal mass at which time excision was performed, and biopsy revealed anorectal mucosal melanoma (AM), anal subtype. Postexcision, 18F-FDG PET/CT identified residual melanoma, confirmed on biopsy. Recurrence was monitored every 3 months using 18F-FDG, which identified a perirectal lymph node 2.5 years later positive for metastatic melanoma. Given the rarity of AM and often delayed diagnosis, patients often present with metastases, resulting in poor prognosis. This unique case of metastatic AM with prolonged survival of 7 years to date supports the implementation of 18F-FDG in the diagnostics and monitoring of AM.
Normative CLEFT-Q Data From the General Dutch Population
Authors: van der Goes Philip A.J. , Van Roey Victor L. , Ombashi Saranda , Mathijssen Irene M.J. , Mink van der Molen Aebele B. , Versnel Sarah L.
Published: November 2024

Patient-Reported Outcome Measures (PROMs), such as the CLEFT-Q, have become essential for outcomes in patients with CL/P. Normative values of the CLEFT-Q for non-CL/P peers have not yet been established. This study aims to establish normative values for the CLEFT-Q in the general Dutch population. Dutch nationals aged 16-24 years without CL/P were recruited through an online survey. Participants completed the CLEFT-Q, excluding the lip scar and eating and drinking scales. Data were weighted based on the Dutch Central Bureau of Statistics. Normative values were calculated as means and standard deviations, stratified by sex and education category. Tobit regression models were used to analyze associations between CLEFT-Q scores and demographic variables. In total, 870 participants responded, of which 160 were excluded due to potential craniofacial anomalies. Significant variations in CLEFT-Q scores based on sex were found, with females scoring lower than males. Level of education had a modest impact on CLEFT-Q scores, with lower education having lower scores on certain scales. Age marginally influenced CLEFT-Q scores, with younger participants scoring lower than older participants. Positive correlations were found between all CLEFT-Q scales. The strongest correlation was observed between the social and school functioning scales. This study provides the first set of normative values for the CLEFT-Q in the Dutch general population. Significant differences in CLEFT-Q scores based on sex, level of education and age were found. These normative values are useful for clinicians interpreting CLEFT-Q scores and help make informed decisions.
Patterns of trauma-induced coagulopathy in injured children: A principal component analysis investigating endothelial, coagulation, and platelet biomarkers
Authors: Morgan Katrina M. , Feeney Erin V. , Spinella Philip C. , Gaines Barbara A. , Leeper Christine M.
Published: November 2024

BACKGROUND

Trauma-induced coagulopathy is common and associated with poor outcomes in injured children. Our aim was to identify patterns of coagulopathy after injury using endothelial, platelet, and coagulation biomarkers, and associate these phenotypes with relevant patient factors and clinical outcomes in a pediatric trauma cohort.

METHODS

Principal component (PC) analysis was performed on data from injured children between 2018 and 2022. Laboratories included endothelial markers (syndecan-1, thrombomodulin, tissue factor, and vascular endothelial growth factor), international normalized ratio, platelet count, rapid thromboelastography maximum amplitude, and base deficit. Variables were reduced to PCs; PC scores were generated for each subject and used in logistic regression with outcomes including mortality, blood transfusion, shock (pediatric-adjusted shock index), and patient characteristics including age, sex, injury mechanism, and traumatic brain injury.

RESULTS

In total, 59 children had complete data for analysis. Median (interquartile range) age was 10 (4–14) years, 31% female, 21% penetrating mechanism, and median (interquartile range) injury severity score of 16 (9–21). Principal component analysis identified two significant PCs accounting for 67% of overall variance. PC1 included syndecan-1, thrombomodulin, vascular endothelial growth factor, international normalized ratio, and base deficit; PC1 scores were associated with mortality, blood transfusion, and shock (all p < 0.001). PC2 included tissue factor, platelet count, and rapid thromboelastography maximum amplitude; PC2 scores were associated with age (ρ = −0.42, p = 0.001) but no studied clinical outcome. Neither PC was significantly associated with sex, injury mechanism, or traumatic brain injury.

CONCLUSION

Principal component analysis detected two distinct biomarker patterns in injured children involving the domains of the endothelium, coagulation, and platelets. The first phenotype was associated with poor clinical outcomes, while the second was associated with age. This supports the concept that pediatric trauma-induced coagulopathy elicits a heterogeneous response, and suggests that there may be a prognostic value to these phenotypes that warrants further investigation.

LEVEL OF EVIDENCE

Prognostic and Epidemiological; Level IV.
TIBIAL OSTEITIS CAUSED BY MYCOBACTERIUM TUBERCULOSIS A CASE REPORT
Authors: benjelloun marwa , Tijani Naji , BenLahlou Yassine , Benaissa Elmostafa , Chadli Mariama Mariama
Published: November 2024

Tuberculosis is a major scourge, posing a serious public health problem in countries where it is endemic. Osteoarticular involvement accounts for 3 to 5% of all tuberculosis cases and 10 to 15% of extrapulmonary tuberculosis cases. We report a case of tibial osteitis caused by Mycobacterium tuberculosis in a 52-year-old female patient who presented to the trauma department at the Mohammed V Military Teaching Hospital with a painful swelling of the lower part of her left leg. Standard X-rays and computed tomography (CT) scans revealed bone involvement, specifically in the tibia. In an endemic context, any persistent and atypical bone lesion should raise suspicion of osteoarticular tuberculosis to enable rapid diagnosis and appropriate therapeutic management. In the absence of other suggestive pulmonary or extrapulmonary lesions, the diagnosis also relies on the exclusion of other pathologies, such as malignant tumors, which may present with similar clinical and radiological features.
Effect of malted millet blends with defatted soybean and cinnamon
flours on physiochemical and bioactive properties
Authors: Ogunjemilusi Motunrayo Abigael , Friday Ogori Akama
Published: November 2024

The study was on physiochemical and bioactive properties of malted millet blends
with defatted soybean and cinnamon flour envisaged for porridge use. The
proximate composition of the blend decreased with malting addition from millet
but increased with soybean flour addition except in ash content. Moisture
content ranged between 8.74-9.00%, crude protein 10.08-12.18%
crude fiber 1.56-2.25%, ash 3.56-2.02% and crude fat content was
3.00-5.75%, respectively. The functional properties of the flour blends
decreased as the inclusion of malted millet increased, but bulk density,
swelling capacity, oil and water absorption capacities of the blends used as
functional porridge increase with soybeans flour ration inclusion. The
antioxidant and anti-diabetes properties of FRAP 0.85-0.47% and
α-amylase 32.20-27.47 g/mL increased with millet malt addition but DPPH
44.68-53.66% and metal chelation 23.73-34.40% and
α-glycosidase 21.49-34.37 g/mL was high as defatted soybean flour
addition increased. Addition of defatted soybean flour on malted millet and
cinnamon flour produced a noticeable effect on the sensory color, taste, flavor,
texture, crispiness and overall acceptability on the porridge produced. Malted
millet addition has less significant effect compared to defatted soybean flour
in making functional and bioactive composite flour porridge production from
millet malting, defatted soybean and cinnamon spice flour blends.
Context-dependent effects of ivermectin residues on dung insects: Interactions with environmental stressors, size, and sex in a sepsid fly (Sepsis neocynipsea)
Authors: Walker Jill , Mathews Benjamin J. , Rohner Patrick T.
Published: November 2024

Insects associated with livestock dung frequently encounter veterinary medication residues. These residues often have negative effects on insect survival, reproduction, and ecosystem functioning and may contribute to the rapid decline in temperate insect populations. Ivermectin is an antiparasitic drug widely used to treat parasites in livestock. While it has long been recognized that ivermectin effects insect survival, the potential interactive effects between ivermectin exposure and other ecologically relevant abiotic stressors remain poorly understood. Here, we study these effects in the black scavenger flySepsis neocynipsea, which depends on cow dung for reproduction. Using a fully factorial design, we test whether the effects of ivermectin exposure on adult survival interact with heat and desiccation stress, and whether these effects depend on size and sex. Ivermectin exposure had strong negative impacts on adult survival, but its effects were stronger in females and large individuals. While heat stress also had a strong effect on adult survival, the combined effects of heat and ivermectin exposure were less severe than the expected additive effects of both stressors applied independently, suggesting some cross-resistance. We did not find an interaction between ivermectin and desiccation stress. Taken together, our findings highlight how the complex interactions between insecticides and abiotic stressors could drive changes in coprophagous insect populations and their ecological functions across different ecosystems and climates.
Learning multi-cellular representations of single-cell transcriptomics data enables characterization of patient-level disease states
Authors: Liu Tianyu , De Brouwer Edward , Kuo Tony , Diamant Nathaniel , Missarova Alsu , Wang Hanchen , Hao Minsheng , Bravo Hector Corrada , Scalia Gabriele , Regev Aviv , Heimberg Graham
Published: November 2024

Single-cell RNA-seq (scRNA-seq) has become a prominent tool for studying human biology and disease. The availability of massive scRNA-seq datasets and advanced machine learning techniques has recently driven the development of single-cell foundation models that provide informative and versatile cell representations based on expression profiles. However, to understand disease states, we need to consider entire tissue ecosystems, simultaneously considering many different interacting cells. Here, we tackle this challenge by generatingpatient-levelrepresentations derived from multi-cellular expression context measured with scRNA-seq of tissues. We develop PaSCient, a novel model that employs a multi-level representation learning paradigm and provides importance scores at the individual cell and gene levels for fine-grained analysis across multiple cell types and gene programs characteristic of a given disease. We apply PaSCient to learn a disease model across a large-scale scRNA-seq atlas of 24.3 million cells from over 5,000 patients. Comprehensive and rigorous benchmarking demonstrates the superiority of PaSCient in disease classification and its multiple downstream applications, including dimensionality reduction, gene/cell type prioritization, and patient subgroup discovery.
Uncovering Bifurcation Behaviors of Biochemical Reaction Systems from Network Topology
Authors: Huang Yong-Jin , Okada Takashi , Mochizuki Atsushi
Published: November 2024

The regulation of biological functions is achieved through the modulation of biochemical reaction network dynamics. The diversity of cell states and the transitions between them have been interpreted as bifurcations in these dynamics. However, due to the complexity of networks and limited knowledge of reaction kinetics, bifurcation behaviors in biological systems remain largely underexplored. To address this, we developed a mathematical method, Structural Bifurcation Analysis (SBA), which decomposes the system into substructures and determines important aspects of bifurcation behaviors—such as substructures responsible for bifurcation conditions, bifurcation-inducing parameters, and bifurcating variables—solely from network topology. We establish a direct relationship between SBA and classical bifurcation analysis, enabling the study of systems even in the presence of conserved quantities. Additionally, we provide a step-by-step bifurcation analysis for general use. We applied our method to the macrophage M1/M2 polarization system. Our analysis reveals that the network structure strongly constrains possible patterns of polarization. We also clarify the dependency of the M1/M2 balance on gene expression levels and predict the emergence of intermediate polarization patterns under gene deletions, including SOCS3, which are experimentally testable.
A deletion at the X-linkedARHGAP36gene locus is associated with the orange coloration of tortoiseshell and calico cats
Authors: Toh Hidehiro , Au Yeung Wan Kin , Unoki Motoko , Matsumoto Yuki , Miki Yuka , Matsumura Yumiko , Baba Yoshihiro , Sado Takashi , Nakamura Yasukazu , Matsuda Miho , Sasaki Hiroyuki
Published: November 2024

The X-linkedorange(O) locus in domestic cats controls an unknown molecular mechanism that causes the suppression of black-brownish pigmentation in favor of orange coloration. The alternating black-brownish and orange patches seen in tortoiseshell and calico cats are considered as classic examples of the phenotypic expression of random X-chromosome inactivation (XCI) occurring in female mammals. However, theOgene in the cat genome has not been identified, and the genetic variation responsible for the orange coloration remains unknown. We report here that a 5.1-kilobase (kb) deletion within an intron of the X-linkedARHGAP36gene, encoding a Rho GTPase activating protein, is closely and exclusively associated with orange coloration. The deleted region contains a highly conserved putative regulatory element, whose removal presumably cause alteredARHGAP36expression. Notably,ARHGAP36expression in cat skin tissues is linked to the suppression of many melanogenesis genes, potentially shifting pigment synthesis from eumelanin to pheomelanin. Furthermore, we find evidence that the gene undergoes XCI in female human and mouse cells, and XCI-dependent CpG island methylation consistent with random XCI in female domestic cats. The 5.1-kb deletion seems widespread in domestic cats with orange coat coloration, suggesting a single origin of this coat color phenotype.
Fungal-derived tRNAs are expressed and aminoacylated in orchid mitochondria
Authors: Warren Jessica M. , Ceriotti Luis F. , Sanchez-Puerta M. Virginia , Sloan Daniel B.
Published: November 2024

Plant mitochondrial genomes (mitogenomes) experience remarkable levels of horizontal gene transfer (HGT), including the recent discovery that orchids anciently acquired DNA from fungal mitogenomes. Thus far, however, there is no evidence that any of the genes from this interkingdom HGT are functional in orchid mitogenomes. Here, we applied a specialized sequencing approach to the orchidCorallorhiza maculataand found that fungal-derived tRNA genes are transcribed, post-transcriptionally modified, and aminoacylated. In contrast, all the transferred protein-coding sequences appear to be pseudogenes. These findings show that fungal HGT has altered the composition of the orchid mitochondrial tRNA pool and suggest that these foreign tRNAs function in translation. The exceptional capacity of tRNAs for HGT and functional replacement is further illustrated by the diversity of tRNA genes in theC. maculatamitogenome, which also include genes of plastid and bacterial origin in addition to their native mitochondrial counterparts.
Host traits and environmental variation shape gut microbiota diversity in wild threespine stickleback
Authors: Härer Andreas , Kurstjens Emma , Rennison Diana J.
Published: November 2024

Background

Despite the growing recognition of the importance of gut microbiota in host ecology and evolution, our understanding of the relative contributions of host-associated and environmental factors shaping gut microbiota composition within and across wild populations remains limited. Here, we investigate how host morphology, sex, genetic divergence, and environmental characteristics influence the gut microbiota of threespine stickleback fish populations from 20 lakes on Vancouver Island, Canada.

Results

Our findings reveal substantial variation in gut microbiota composition and diversity among populations, with host traits exerting a stronger influence on bacterial alpha diversity than environmental characteristics. Host morphology, which is indicative of trophic ecology, was linked to gut microbiota divergence among populations, suggesting that dietary specialization may play a role in shaping the stickleback gut microbiota. Within and across populations, we only observed a weakly defined core microbiota and limited sharing of ASVs among hosts, indicating that gut microbiota composition is individualized. Additionally, we detected sex-dependent differences in microbial diversity, opening avenues for future research into the mechanisms driving this variation.

Conclusions

In sum, our study emphasizes the need to consider both host-associated and environmental factors in shaping gut microbiota dynamics and highlights the complex interplay between host organisms, their associated microbial communities, and the environment in natural settings. Ultimately, these insights enhance our understanding of host-microbiota interactions and their eco-evolutionary implications.
Cellular behavior analysis from live-cell imaging of TCR T cell–cancer cell interactions
Authors: Verma Archit , Yu Changhua , Bachl Stefanie , Lopez Ivan , Schwartz Morgan , Moen Erick , Kale Nupura , Ching Carter , Miller Geneva , Dougherty Tom , Pao Ed , Graf William , Ward Carl , Jena Siddhartha , Marson Alex , Carnevale Julia , Van Valen David , Engelhardt Barbara E
Published: November 2024

T cell therapies, such as chimeric antigen receptor (CAR) T cells and T cell receptor (TCR) T cells, are a growing class of anti-cancer treatments. However, expansion to novel indications and beyond last-line treatment requires engineering cells’ dynamic population behaviors. Here we develop the tools forcellular behavior analysisof T cells from live-cell imaging, a common and inexpensive experimental setup used to evaluate engineered T cells. We first develop a state-of-the-art segmentation and tracking pipeline,Caliban, based on human-in-the-loop deep learning. We then build theOccidentpipeline to collect a catalog of phenotypes that characterize cell populations, morphology, movement, and interactions in co-cultures of modified T cells and antigen-presenting tumor cells. We use Caliban and Occident to interrogate how interactions between T cells and cancer cells differ when beneficial knock-outs ofRASA2andCUL5are introduced into TCR T cells. We apply spatiotemporal models to quantify T cell recruitment and proliferation after interactions with cancer cells. We discover that, compared to a safe harbor knockout control,RASA2knockout T cells have longer interaction times with cancer cells leading to greater T cell activation and killing efficacy, whileCUL5knockout T cells have increased proliferation rates leading to greater numbers of T cells for hunting. Together, segmentation and tracking from Caliban and phenotype quantification from Occident enable cellular behavior analysis to better engineer T cell therapies for improved cancer treatment.
Chaperonin TRiC bridges radial spokes for folding proteins locally translated in mammalian sperm flagella
Authors: Meng Xueming , Li Luan , Lin Cheng , Zhu Yun , Feng Yanyan , Zhou Xuehai , Tong Yujie , Wang Shanshan , Yin Guoliang , Liu Ruimin , Sun Fei , Yan Xiumin , Zhu Xueliang , Cong Yao
Published: November 2024

As animals evolved from external to internal fertilization, sperm flagella, which once transiently propelled sperm in water to reach nearby eggs, developed to beat for days or even longer within the female reproductive tract. How flagella were remodeled accordingly remains unclear. Unlike externally fertilizing zebrafish and sea urchin, mammalian sperm flagella feature a unique barrel-shaped bridge between axonemal radial spokes RS1 and RS2, though its components and function remain unknown. Here, using cryo-EM and cryo-ET combined with mass spectrometry and immunofluorescence staining, we reveal that this RS1-RS2 barrel (RRB) in mammalian sperm flagella is a group II chaperonin TRiC/CCT. We purified and resolved the unforeseen cryo-EM structure of TRiC from bovine sperm flagella, discovering that flagella TRiC contains the testis-specific CCT6B subunit. Additionally, we resolved the cryo-ET map of mouse sperm flagella RSs, containing the RRB, achieving unprecedented local resolution of 10-14 Å. Thein-situRRB map displays two extra densities within its chambers in a polarized manner, suggesting the presence of folding substrates and a co-chaperone (likely phosducin-like 2). Notably, mammalian flagella also contain components of translation machineries and actively synthesize proteins. Our results suggest that the RRB TRiC folds locally translated proteins to sustain mammalian flagella, providing new insights into flagellar remodeling in internally fertilizing species. Our findings also shed lights on male fertility and potential treatments for infertility.
Smartphone Postural Sway and Pronator Drift tests as Measures of Neurological Disability
Authors: Calcagni Michael , Kosa Peter , Bielekova Bibi
Published: November 2024

The COVID-19 pandemic and increased demands for neurologists have inspired the creation of remote, digitalized tests of neurological functions. This study investigates two tests from the Neurological Functional Tests Suite (NeuFun-TS) smartphone application, the “Postural Sway” and “Pronator Drift” tests. These tests capture different domains of postural control and motoric dysfunction in healthy volunteers (n=13) and people with neurological disorders (n=68 relapsing-remitting multiple sclerosis [MS]; n=21 secondary progressive MS; n=23 primary progressive MS; n=13 other inflammatory neurological diseases; n=21 non-inflammatory neurological diseases; n=4 clinically isolated syndrome; n=1 radiologically isolated syndrome). Smartphone accelerometer data was transformed into digital biomarkers, which were filtered in the training cohort (∼80% of subjects) for test-retest reproducibility and correlations with subdomains of neurological examinations and validated imaging biomarkers. The independent validation cohort (∼20%) determined whether biomarker models outperformed the best single digital biomarkers. Postural sway acceleration magnitude in the eyes closed and feet together stance demonstrated the highest reliability (ICC=.706), strongest correlations with age (Pearson r<=.82) and clinical and imaging outcomes (r<=.65, p<0.001) and stronger predictive value for sway-relevant neurological disability outcomes than models that aggregated multiple biomarkers (coefficient of determination R2=.46 vs .38). The pronator drift test only captured cerebellar dysfunction, had less reproducible biomarkers, but provided additive value when combined with postural sway biomarkers into models predicting global scales of neurological disability. In conclusion, a simple 1-minute postural sway test accurately measures body oscillations that increase with natural aging and differentiates them from abnormally increased body oscillations in people with neurological disabilities.
Evaluation of a commercial Multiplex Real-Time PCR Assay for orthopoxvirus and monkeypox virus detection, and simultaneous subclade Ib identification
Authors: Wawina-Bokalanga Tony , Haesler Michael , Akil-Bandali Prince , Ola-Mpumbe Rilia , Kinganda-Lusamaki Eddy , Makangara-Cigolo Jean-Claude , Pukuta-Simbu Elisabeth , Cikaya-Kankolongo Fiston , Mapenzi-Kashali Nelson , Ponga-Museme Ange , de Block Tessa , Lumembe-Numbi Raphaël , Amuri-Aziza Adrienne , Luakanda Gradi , Jansen Daan , Vercauteren Koen , Ahuka-Mundeke Steve , Schuchmann Kai , Mbala-Kingebeni Placide , Muyembe-Tamfum Jean-Jacques
Published: November 2024

Several mpox outbreaks, caused by subclades Ia and Ib monkeypox virus (MPXV), are ongoing in the Democratic Republic of the Congo. The World Health Organization declared the ongoing mpox outbreak a Public Health Emergency of International Concern due to the geographic expansion of subclade Ib. We assessed the performance of a novel multiplex real-time PCR assay designed for MPXV detection and simultaneous subclade Ib identification. This assay demonstrates high accuracy and specificity, underscoring its use for the current mpox outbreak.
Engineering assembloids to mimic graft-host skeletal muscle interaction
Authors: Rossi Lucia , Auletta Beatrice , Placa Marco La , Cecconi Giada , Chiolerio Pietro , Maghin Edoardo , Angiolillo Silvia , Carraro Eugenia , Gagliano Onelia , Laterza Cecilia , Elvassore Nicola , Piccoli Martina , Urciuolo Anna
Published: November 2024

Skeletal muscle (SkM) tissue engineering aims to generate in vitro three-dimensional (3D) products that can be implanted in patients to replace or repair damaged muscles. Having a humanized in vitro model able to mimic the interaction between the innervated recipient and the engineered SkMs at a functional level would greatly help in the evaluation of the graft potential.

Here we developed a 3D in vitro model that allowed to investigate the function, stability, and adaptability of the human NM system in response to an engineered SkM construct. To achieved this, we used decellularized SkMs (dSkM)-based constructs as engineered SkM and human neuromuscular organoids (NMOs) as the recipient-like NM system to create graft-host SkM assembloids.

We observed migration of myogenic cells and invasion of neural axons from the NMO to the engineered SkM construct in the assembloids, with the generation of functional neuromuscular junctions (NMJs). Finally, we showed that assembloids were able to regenerate following acute damage, with SkM regeneration and functional recovery.

Despite limited by the absence of immunocompetent cells and vasculature, our data showed that our assembloid represents a useful tool to evaluate in vitro the response of the human innervated SkM to a potential tissue-engineered SkM graft.
Single-cell spatial mapping reveals alteration of cell type composition and tissue microenvironment during early colorectal cancer formation
Authors: Guha Tuhin K. , Esplin Edward D. , Horning Aaron M. , Chiu Roxanne , Paul Kristina , Weimer Annika K. , Becker Winston R. , Laquindanum Rozelle , Mills Meredith A. , Esplin D. Glen , Shen Jeanne , Monte Emma , White Shannon , Karathanos Thomas V. , Cotter Daniel , Bi Joanna , Ladabaum Uri , Longacre Teri A. , Curtis Christina , Greenleaf William J. , Ford James M. , Snyder Michael P.
Published: November 2024

Colorectal cancer (CRC) is the third leading cause of cancer mortality in the United States. Familial adenomatous polyposis (FAP) is a hereditary syndrome that raises the risk of developing CRC, with total colectomy as the only effective prevention. Even though FAP is rare (0.5% of all CRC cases), this disease model is well suited for studying the early stages of malignant transformation as patients form many polyps reflective of pre-cancer states. In order to spatially profile and analyze the pre-cancer and tumor microenvironment, we have performed single-cell multiplexed imaging for 52 samples: 12 normal mucosa,16 FAP mucosa,18 FAP polyps, 2 FAP adenocarcinoma, and 4 sporadic colorectal cancer (CRCs) using Co-detection by Indexing (CODEX) imaging platform. The data revealed significant changes in cell type composition occurring in early stage polyps and during the malignant transformation of polyps to CRC. We observe a decrease in CD4+/CD8+ T cell ratio and M1/M2 macrophage ratio along the FAP disease continuum. Advanced dysplastic polyps show a higher population of cancer associated fibroblasts (CAFs), which likely alter the pre-cancer microenvironment. Within polyps and CRCs, we observe strong nuclear expression of beta-catenin and higher number neo-angiogenesis events, unlike FAP mucosa and normal colon counterparts. We identify an increase in cancer stem cells (CSCs) within the glandular crypts of the FAP polyps and also detect Tregs, tumor associated macrophages (TAMs) and vascular endothelial cells supporting CSC survival and proliferation. We detect a potential immunosuppressive microenvironment within the tumor ‘nest’ of FAP adenocarcinoma samples, where tumor cells tend to segregate and remain distant from the invading immune cells. TAMs were found to infiltrate the tumor area, along with angiogenesis and tumor proliferation. CAFs were found to be enriched near the inflammatory region within polyps and CRCs and may have several roles in supporting tumor growth. Neighborhood analyses between adjacent FAP mucosa and FAP polyps show significant differences in spatial location of cells based on functionality. For example, in FAP mucosa, naive CD4+ T cells alone tend to localize near the fibroblast within the stromal compartment. However, in FAP polyp, CD4+T cells colocalize with the macrophages for T cell activation. Our data are expected to serve as a useful resource for understanding the early stages of neogenesis and the pre-cancer microenvironment, which may benefit early detection, therapeutic intervention and future prevention.
Automated identification of small molecules in cryo-electron microscopy data with density- and energy-guided evaluation
Authors: Muenks Andrew , Farrell Daniel P. , Zhou Guangfeng , DiMaio Frank
Published: November 2024

Methodological improvements in cryo-electron microscopy (cryoEM) have made it a useful tool in ligand-bound structure determination for biology and drug design. However, determining the conformation and identity of bound ligands is still challenging at the resolutions typical for cry-oEM. Automated methods can aid in ligand conformational modeling, but current ligand identification tools — developed for X-ray crystallography data — perform poorly at resolutions common for cryoEM. Here, we present EMERALD-ID, a method capable of docking and evaluating small molecule conformations for ligand identification. EMERALD-ID identifies 43% of common ligands exactly and identifies closely related ligands in 66% of cases. We then use this tool to discover possible ligand identification errors, as well as previously unidentified ligands. Furthermore, we show EMERALD-ID is capable of identifying ligands from custom ligand libraries of various small molecule types, including human metabolites and drug fragments. Our method provides a valuable addition to cryoEM modeling tools to improve small molecule model accuracy and quality.
Deficits in forelimb reach learning in a mouse model of Fragile X syndrome
Authors: Young Leanne F. , Derham Ann , Zhu Rui , Suvrathan Aparna
Published: November 2024

Fragile X syndrome is a leading cause of intellectual disability and autism spectrum disorder, for which therapies are limited. A mouse model of Fragile X syndrome, theFmr1knockout (KO) mouse, has been particularly valuable for interrogating the molecular, cellular, and circuit mechanisms that underlie the neurological deficits seen in this syndrome. Key deficits in Fragile X syndrome include impairments in social behaviors, cognition, and motor learning. Given the difficulties in extrapolating more complex human behaviors to mouse models, simple motor behaviors are a particularly tractable form of learning to study in the mouse. We investigated a form of forelimb reach learning inFmr1KO mice, precisely quantifying different parameters of the task using both manual analysis and DeepLabCut-based tracking of reach trajectories. WhileFmr1KO mice show impaired learning overall, our results demonstrated that the presence or absence of a cue that signals reward alleviates some of the deficits. In addition to a single metric of success in learning, we determined the specific parameters of the motor behavior that were responsible for that success or failure. In particular, our results suggested thatFmr1KO mice showed impaired improvement in the trajectory of the reach, reflected by a greater likelihood of completely missing the target, and in a lower learning index for the optimal reach trajectory. In addition, we fully described the features underlying learning, including categorizing the first attempt during trials, failed reaches where mice make contact with the reward, the number of trials where no attempts were made, as well as how the pattern of these different behaviors varies inFmr1KO mice. Our findings provide an essential framework for linking specific behavioral impairments in motor learning to the cellular and circuit mechanisms that support them.
Deep learning from videography as a tool for measuringE. coliinfection in poultry
Authors: Scheidwasser Neil , Poulsen Louise Ladefoged , Leow Prince Ravi , Khurana Mark Poulsen , Iglesias-Carrasco Maider , Laydon Daniel Joseph , Donnelly Christl Ann , Bojesen Anders Miki , Bhatt Samir , Duchêne David Alejandro
Published: November 2024

Poultry farming is threatened by regular outbreaks ofEscherichia coli(E. coli) that lead to significant economic losses and public health risks. However, traditional surveillance methods often lack sensitivity and scalability. Early detection of infected poultry using minimally invasive procedures is thus essential for preventing epidemics. To that end, we leverage recent advancements in computer vision, employing deep learning-based tracking to detect behavioural changes associated withE. coliinfection in a case-control trial comprising two groups of 20 broiler chickens: (1) a healthy control group and (2) a group infected with a pathogenicE. colifield strain from the poultry industry. More specifically, kinematic features derived from deep learning-based tracking data revealed markedly reduced activity in the challenged group compared to the negative control. These findings were validated by lower mean optical flow in the infected flock, suggesting reduced movement and activity, and post-mortem physiological markers of inflammation which confirmed the severity of infection in the challenged group. Overall, this study demonstrates that deep learning-based tracking offers a promising solution for real-time monitoring and early infection detection in poultry farming, with the potential to help reduce economic losses and mitigate public health risks associated with infectious disease outbreaks in poultry.
Coagulative Granular Hydrogels with an Enzyme Catalyzed Fibrin Network for Endogenous Tissue Regeneration
Authors: Deng Zhipeng , Tovani Camila B. , Bianco Simona , Comandini Gianni , Elghajiji Aya , Adams Dave J. , Scarpa Fabrizio , Whitehouse Michael R. , Seddon Annela M. , Armstrong James P. K.
Published: November 2024

Granular hydrogels, composed of densely packed microgels, are an emerging class of injectable microporous scaffolds that provide interstitial porosity for endogenous cell recruitment and tissue repair. However, weak bonding interactions between constituent microgels compromises the mechanical integrity of these biomaterials, limiting their scope and effectiveness forin vivoapplication where structural support is required. To address this challenge, we introduce a new bioinspired stabilization method and a novel class of regenerative biomaterial:coagulative granular hydrogels, assembled from thrombin-functionalized gelatin methacryloyl microgels. The surface-bound thrombin is enzymatically active and catalyzes the conversion of fibrinogen into a fibrin hydrogel that extends throughout the interstitial voids of the granular hydrogel. This secondary network acts as a biological glue to stabilize the granular hydrogel, yielding shear and compressive properties comparable to bulk hydrogel controls. Furthermore, the interstitial fibrin network provides a favorable microenvironment for the adhesion, proliferation, and invasion of endothelial cells, highlighting the potential of the biomaterial to support endogenous tissue repair. This innovative stabilization mechanism provides a responsive biomaterial system, and future studies will seek to explore how the biomaterial is annealedin vivoby the presence of blood plasma fibrinogen.
Wind Tunnel Study of the Forces Due to Drafting in Dolphin Mother-Calf pairs
Authors: Weihs D. , Ringel M.
Published: November 2024

Cetacean calves can get assistance in rapid swimming by drafting with the mothers. The hydrodynamic forces produced have been predicted to enable reducing the drag on the calf Using models in a wind tunnel, the similarity between motion in the air and submerged swimming is used to produce quantitative data on the reduction of drag due to drafting in accordance with the theoretical predictions.