bluuebunny/crossref_metadata_2025 huggingface dataset:
Bioaugmentation to enhance degradation of acetochlor and pretilachlor in water and sediment under anaerobic conditions
Authors: Duc Ha Danh , Oanh Nguyen Thi
Published: December 2024

Chloroacetamide herbicides are widely used to control weeds globally. In this study, three acetochlor-degrading mixed cultures using nitrate, sulfate, and ferric iron as electron acceptors were isolated and determined for their degradation under anaerobic conditions. The degradation rates of all mixed pure cultures in a mineral medium were not much different at 1 µM, while the rates at 50 µM were in the order: mixed culture using nitrate > sulfate > ferric iron as electron acceptors, giving 6.70, 6.13, and 4.85 µM/day, respectively. During acetochlor degradation, 2-ethyl-6-methyl-N-(ethoxymethyl)acetanilide, N-2-ethylphenyl acetamide, and 2-ethylaniline were transiently produced. Interestingly, the mixture of all cultures synergistically degraded pretilachlor although no individual strains could degrade the compound. Toluene and 2-ethylaniline were metabolites of pretilachlor degradation by the acetochlor-degrading bacteria. However, pretilachlor inhibited the acetochlor degradation by acetochlor-degrading bacteria. The inoculation of both acetochlor- and pretilachlor-degrading bacteria resulted in 91.4 ± 2.1% of acetochlor and 82.4 ± 2.6% of pretilachlor being utilized for 7 days. Moreover, the introduction of these degrading bacteria accelerated the degradation of both substrates contaminating water and sediment collected from a pond. This study provides insights into anaerobic degradation by pure cultures using different electron acceptors.
A novel method for telomere length detection in fission yeast
Authors: Mohamed Hadeel A B Elnaim , Agus Hizlan Hincal , Palabiyik Bedia
Published: December 2024

Fission yeast is the ideal model organism for studying telomere maintenance in higher eukaryotes. Telomere length has been directly correlated with life expectancy and the onset of aging-related diseases in mammals. In this study, we developed a novel simple, and reproducible method to measure the telomere length, by investigating the effect of caffeine and cisplatin on the telomere length in fission yeast. Hydroxyurea-synchronized fission yeast cells were exposed to 62 µM cisplatin and 8.67 mM caffeine treatments for 2 h, then their telomere lengths were evaluated with two different methods. First, the quantitative polymerase chain reaction (qPCR) assay was used as a confirmative method, where telomere length was determined relative to a single-copy gene in the genome. Second, the newly developed method standard polymerase chain reaction (PCR)/ImageJ assay assessed the telomere length based on the amplified PCR band intensity using a set of telomere primers, reflecting telomeric sequence availability in the genome. Both methods show a significant decrease and a notable telomere lengthening in response to cisplatin and caffeine treatments, respectively. The finding supports the accuracy and productivity of the standard PCR/ImageJ assay as it can serve as a quick screening tool to study the effect of suspected chemotherapeutic and antiaging drugs on telomere length in fission yeast.
Acute Severe Ulcerative Colitis and Cytomegalovirus During Pregnancy: A Case Report
Authors: Lelong Margaux , Bourreille Arnaud , Mosnier Jean-François , Trang-Poisson Caroline , Le Berre Catherine
Published: December 2024

Lay Summary

This is the first case report of cytomegalovirus colitis following viral reactivation during pregnancy in a patient hospitalized for acute severe ulcerative colitis and treated with ganciclovir despite its teratogenic risk given her corticosteroid-refractory nature, with favorable outcomes after 3 years.
Listening and Preparing the Society to Engage: The Case of the Colombian Truth Commission and Its Legacy Strategy
Authors: Prada Ramírez María Paula , Wingender Leslie
Published: December 2024

Reflections on the Colombian Truth Commission are timely to answer a question less explored in the transitional justice literature related to how transitional justice processes have been popularized and made accessible to the broader public, and moreover, how the various stakeholders have extended the fruits of transitional justice. In this note from the field, we offer our practitioner perspectives on the key enabling conditions and strategic moments in the development of the Commission’s legacy strategy that contributed to these outcomes. We examine how the Commission’s ethical and political framing of the listening exercises and its overall institutional structure led to a long-term peacebuilding project that continues to mobilize today through the work of the Trabajo en red con aliados or the Network of Allies. We unpack the key factors that foster ongoing mobilization of civil society and local government actors engaged in debating, implementing and grappling with the recommendations of the final report. This note provides new information for the debate about the value of networks and partnerships related to facing the truth and moving towards non-recurrence in transitional justice endeavors.
Host plant selection and performance of ambrosia beetles in flood-stressed versus ethanol-injected trees provide implications for management strategies
Authors: Cambronero-Heinrichs Juan Carlos , Ranger Christopher M , Santoiemma Giacomo , Cavaletto Giacomo , Carloni Francesca , Battisti Andrea , Meggio Franco , Rassati Davide
Published: December 2024

Ambrosia beetles (Curculionidae: Scolytinae and Platypodinae) are fungus-farming woodborers that can cause damage to the trees they colonize. Some of these beetles target stressed plants that emit ethanol, and management strategies have proposed using ethanol-injected trees as trap trees to monitor or divert dispersing adult females away from valuable crops. In this study, we used container-grown trees from 8 species to compare the effect of ethanol injection versus flooding on ambrosia beetle host selection and colonization success. Our aims were to understand whether ethanol injection is a suitable technique for different ambrosia beetle species and whether its effectiveness varies depending on the tree species used. In addition, we quantified the amount of ethanol in tree tissues to understand whether ethanol concentration could reflect observed differences among treatments and tree species. Our findings demonstrated that ethanol-injected trees were significantly more selected by both Xyleborinus saxesenii and Xylosandrus spp. and that significantly more adult beetles of both taxa emerged from ethanol-injected than flood-stressed trees. In addition, we showed that ethanol injection can trigger attacks by X. saxesenii and Xylosandrus spp. on a variety of deciduous tree species, nullifying the effects of the species-specific characteristics observed on flood-stressed trees, which can only partially be attributed to the amount of ethanol within the plant. This supported the idea that practitioners can potentially select any species of deciduous trees in management programs for ambrosia beetles based on ethanol-injected trees.
Probabilistic inference of the structure and orbit of Milky Way satellites with semi-analytic modelling
Authors: Folsom Dylan , Slone Oren , Lisanti Mariangela , Jiang Fangzhou , Kaplinghat Manoj
Published: December 2024

Semi-analytic modelling furnishes an efficient avenue for characterizing dark matter haloes associated with satellites of Milky Way-like systems, as it easily accounts for uncertainties arising from halo-to-halo variance, the orbital disruption of satellites, baryonic feedback, and the stellar-to-halo mass (SMHM) relation. We use the SatGen semi-analytic satellite generator, which incorporates both empirical models of the galaxy–halo connection as well as analytic prescriptions for the orbital evolution of these satellites after accretion onto a host to create large samples of Milky Way-like systems and their satellites. By selecting satellites in the sample that match observed properties of a particular dwarf galaxy, we can infer arbitrary properties of the satellite galaxy within the cold dark matter paradigm. For the Milky Way’s classical dwarfs, we provide inferred values (with associated uncertainties) for the maximum circular velocity $v_\text{max}$ and the radius $r_\text{max}$ at which it occurs, varying over two choices of baryonic feedback model and two prescriptions for the SMHM relation. While simple empirical scaling relations can recover the median inferred value for $v_\text{max}$ and $r_\text{max}$, this approach provides realistic correlated uncertainties and aids interpretability. We also demonstrate how the internal properties of a satellite’s dark matter profile correlate with its orbit, and we show that it is difficult to reproduce observations of the Fornax dwarf without strong baryonic feedback. The technique developed in this work is flexible in its application of observational data and can leverage arbitrary information about the satellite galaxies to make inferences about their dark matter haloes and population statistics.
Dusty substructures induced by planets in ALMA discs: how dust growth and dynamics changes the picture
Authors: Ziampras Alexandros , Sudarshan Prakruti , Dullemond Cornelis P , Flock Mario , Berta Vittoria , Nelson Richard P , Mignone Andrea
Published: December 2024

Protoplanetary discs exhibit a rich variety of substructure in millimeter continuum emission, often attributed to unseen planets. As these planets carve gaps in the gas, dust particles can accumulate in the resulting pressure bumps, forming bright features in the dust continuum. We investigate the role of dust dynamics in the gap-opening process with 2D radiation hydrodynamics simulations of planet–disc interaction and a two-population dust component modelled as a pressureless fluid. We consider the opacity feedback and backreaction due to drag forces as mm grains accumulate in pressure bumps at different stages of dust growth. We find that dust dynamics can significantly affect the resulting substructure driven by the quasi-thermal-mass planet with $M_\mathrm{p}/M_\star =10^{-4}$. Opacity feedback causes non-axisymmetric features to become more compact in azimuth, whereas the drag-induced backreaction tends to dissolve non-axisymmetries. For our fiducial model, this results in multiple concentric rings of dust rather than the expected vortices and corotating dust clumps found in models without dust feedback. A higher coagulation fraction disproportionately enhances the effect of dust opacity feedback, favouring the formation of crescents rather than rings. Our results suggest that turbulent diffusion is not always necessary to explain the rarity of observed non-axisymmetric features, and that incorporating dust dynamics is vital for interpreting the observed substructure in protoplanetary discs. We also describe and test the implementation of the publicly available dust fluid module in the pluto code.
Passive thermal management system for electric-hybrid vehicles—hot climate condition
Authors: Şahan Nurten , Paksoy Halime
Published: December 2024

To achieve net-zero emissions targets, electric vehicles and hybrid electric vehicles are prioritized for reducing CO₂ emissions in transportation. Among the available battery systems, lithium-based batteries are the most prominent due to their high energy storage density. The primary safety risk in lithium-ion batteries is thermal instability caused by overheating. Battery capacity drops significantly at operating temperatures >45°C. At higher temperatures, the battery undergoes thermal decomposition, and once it reaches a critical temperature, it enters an irreversible state of thermal instability, which can lead to an explosion. In our previous study, we developed flexible phase-change material (PCM) packages for passive thermal energy storage of heat from lithium-ion batteries in hybrid electric vehicles/electric vehicles, extending battery life and ensuring safety. In this paper, we present the results of applying these PCM packages under hot climate conditions. The test results show that both paraffin and composite PCMs can maintain lower temperatures compared to battery modules without PCM, ensuring safe operation. The PCM composite, which includes highly conductive materials, demonstrated better thermal performance than paraffin alone.
Cell-free tumor DNA analysis in advanced or metastatic breast cancer patients: mutation frequencies, testing intention, and clinical impact
Authors: Huebner Hanna , Wimberger Pauline , Laakmann Elena , Ruckhäberle Eugen , Ruebner Matthias , Lehle Sarah , Uhrig Sabrina , Ziegler Philipp , Link Theresa , Hack Carolin C , Belleville Erik , Faull Iris , Hausch Marcus , Wallwiener Diethelm , Schneeweiss Andreas , Tesch Hans , Brucker Sara Y , Beckmann Matthias W , Fasching Peter A , Müller Volkmar , Fehm Tanja N
Published: December 2024

Background

Circulating cell-free tumor DNA (ctDNA) provides a non-invasive approach for assessing somatic alterations. The German PRAEGNANT registry study aims to explore molecular biomarkers and investigate their integration into clinical practice. In this context, ctDNA testing was included to understand the motivations of clinicians to initiate testing, to identify somatic alterations, and to assess the clinical impact of the results obtained.

Methods

Patients with advanced/metastatic breast cancer were prospectively enrolled in the Prospective Academic Translational Research Network for the Optimization of Oncological Health Care Quality in the Adjuvant and Advanced/Metastatic Setting (PRAEGNANT study; NCT02338167). The FDA-approved and CE-marked GUARDANT360 CDx test was used to assess somatic alterations. A ctDNA-analysis report was provided to the treating physician along with a questionnaire about the intent for testing and the clinical implications of test results.

Results

ctDNA from 49 patients was analyzed prospectively: 37 (76%) had at least one somatic alteration in the analyzed geneset; 14 patients (29%) harbored alterations in TP53, 12 (24%) in PIK3CA, and 6 (12%) in ESR1. Somatic mutations in BRCA1 or BRCA2 were detected in 3 (6%) and 4 (8%) patients, respectively, and 59% of patients had hormone receptor-positive, human epidermal growth factor receptor 2-negative breast cancer. Questionnaires regarding test intentions and clinical impact were completed for 48 (98%) patients. These showed that ctDNA testing influenced treatment decisions for 35% of patients.

Discussion

The high prevalence of somatic alterations in TP53, PIK3CA, ESR1, and BRCA1/2 genes, identified by ctDNA genotyping, highlights their potential as biomarkers for targeted therapies. Detection of specific mutations affected treatment decisions, such as eligibility for alpelisib, and might further facilitate treatment with e.g. elacestrant or capiversatib in future treatment lines.
The spectrometer development of CosmoCube, lunar orbiting satellite to detect 21-cm hydrogen signal from cosmic dark ages
Authors: Artuc Kaan , de Lera Acedo Eloy
Published: December 2024

The cosmic Dark Ages represent a pivotal epoch in the evolution of the Universe, marked by the emergence of the first cosmic structures under the influence of dark matter. The 21-cm hydrogen line, emanating from the hyperfine transition of neutral hydrogen, serves as a critical probe into this era. We describe the development and implementation of the spectrometer for CosmoCube, a novel lunar orbiting CubeSat designed to detect the redshifted 21-cm signal within the redshift range of 13 to 150. Our instrumentation utilizes a Xilinx Radio Frequency System-on-Chip (RFSoC), which integrates both Analog-to-Digital Converters (ADCs) and Digital-to-Analog Converters (DACs), tailored for the spectrometer component of the radiometer. This system is characterized by a 4096 FFT length at 62.5 kHz steps using a Polyphase Filter Bank (PFB), achieving an average Effective Number of Bits (ENOB) of 11.5 bits throughout the frequency of interest, from 10 to 100 MHz. The spectrometer design is further refined through loopback tests involving both DAC and ADC of the RFSoC, with DAC outputs varying between high (+1 dBm) and low (−3 dBm) power modes to characterize system performance. The power consumption was optimized to 5.45 W using three ADCs and one DAC for the radiometer. Additionally, the stability of the ADC noise floor was investigated in a thermal chamber with environmental temperatures ranging from 5 to 40 $^{\circ }$C. A consistent noise floor of approximately −152.5 dBFS/Hz was measured, with a variation of $\pm$0.2 dB, ensuring robust performance under varying thermal conditions.
Telescope arrays for wide-field sky surveys. A technical assessment and a cost model
Authors: Buzzoni Alberto
Published: December 2024

In this study we tackled a proxy approach to wide-field large monolithic telescopes in terms of composite assembly of smaller instruments. As a conveniently ‘fast’ f-number is the ultimate parameter to efficiently carry out inspection of large portions of sky, we show that a telescope array can provide a cost-effective solution, as a factor of $\sqrt N $ reduced f-number can be achieved when combining N (similar) telescopes, each of diameter darray, to synthesize an equivalent monolithic diameter ${D}_{\rm{mono}} = \sqrt N {d}_{\rm {array}}$. A cost model is developed, in this regard, by comparing the COTS figures for telescopes up to a metric size as supplied by primary international manufacturers. If a standard cost versus diameter relationship is assumed, in the form C∝Dn, then data indicate that n = 2.5 ± 0.4. In addition, a more realistic multiparametric dependence is assumed, including the f-number, in the form $C \propto {( {{{{D}^3} {/ {\vphantom {{{D}^3} f}}} f}} )}^m$, with m = 0.70 ± 0.08. This eventually leads us to estimate that cost of the optical tube assembly (OTA) for commercial telescopes scales as C∝D2.10 ± 0.24f−0.70 ± 0.08. Even considering the supplementary addition of CCD/CMOS detectors for a telescope array, a general saving scheme confirms that any array solution with N ≥ 4 telescopes, each with a diameter in excess to 30–40 cm, could be a competitive alternative to a bigger monolithic instrument of metric class (or larger), mainly aimed at wide-field surveys.
Associations between Klotho levels, and KL-VS Heterozygosity and Cognition in Schizophrenia
Authors: Majumdar Vijaya , Chakrobarty Prosenjeet , Arasappa Rashmi , Murugesh K , Hegde Shanthala , Jose Amrutha , Manjunath N K , Dharmappa Arpitha
Published: December 2024

Background and Hypothesis

The relationship between Klotho and cognitive dysfunction in schizophrenia has been scarcely explored, with a few paradoxical findings. Hence, we aimed to enhance the understanding of the same by testing associations both for the functional KL-VS gene variant and circulating protein levels.

Research design

This case-control study included 239 healthy controls and 241 patients with schizophrenia, who were comprehensively characterised by neurocognitive tests and further subtyped into cognitive clusters; cognitively deficient and cognitively spared, using K-means cluster analysis. Heterozygotes for the KL-VS haplotype were compared with non-carriers using linear regression models to assess the main effect of the KL-VS heterozygosity (KL-VSHet+)/KL levels and with the interaction terms to understand the influence of variables like disease status and age, on cognition.

Results

There was no main effect of KL-VSHet+ on cognitive domains, but the CD cluster exhibited strong negative interactions between SZ status and Klotho for executive function at the gene level, KL-VSHet+ x disease status, β=-0.61, P=0.043, and comparatively higher effect for KL levels, KL levels x disease status, β=-0.91, P=0.028. There was an opposing positive interaction for response inhibition, KL-VSHet+ x disease status, limited again to the CD cluster, β= 0.35, P=0.046, with a higher magnitude at protein levels, β=0.72, <0.004, though without CD cluster-effect.

Conclusions

Overall, these dissociable patterns of association across cognitive subtypes indicate the need to exert caution over accepting any generalized effect of KL-VS heterozygosity and Klotho levels on cognition and considering the plausible population- and domain-specific effects for clinical decisions.
Effect of hempseed meal on health, growth performance, ruminal fermentation, and carcass traits of intact male goats
Authors: Ale Khim B , Abrahamsen Frank W , Goetsch Arthur L , Sawyer Jason T , Bolden-Tiller Olga , Okere Chukwuemeka , Gurung Reshma , Chaudhary Santosh , Gurung Nar K
Published: December 2024

Hempseed meal (HSM) is a potential alternative feedstuff for livestock due to its high protein content, but it has not been approved for animal feed in the United States due to safety concerns. This study was conducted to determine the effects of HSM on feed intake, growth performance, serum biochemistry, ruminal papillae morphology, ruminal fermentation profiles, and carcass characteristics of intact male goats. Thirty-six Boer × Spanish intact male goats were randomly assigned to one of four experimental diets (n = 9 goats/diet): 0%, 10%, 20%, and 30% HSM on as-fed basis. Diets were formulated to be isonitrogenous and fed free-choice for ad libitum consumption in the 60-day experiment. Linear and quadratic effects of different concentrations of HSM were determined. Total feed intake, crude protein intake, ruminal papillae morphology (papillae density, length, width, absorptive surface area, stratum corneum, and stratum granulosum thickness), carcass traits (longissimus muscle area, body wall thickness, backfat thickness, shrink percentage), and serum concentrations of most metabolites were similar among treatments (P > 0.05). Intake of acid detergent fiber (ADF) and nitrogen detergent fiber (NDF) increased linearly (P < 0.05) with increasing inclusion of HSM in the diet. Average daily gain (ADG), gain-to-feed ratio, and dressing percentage decreased linearly (P < 0.05) with an increasing percentage of HSM in the diet. Similarly, concentrations of propionic, butyric, iso-butyric, valeric, and isovaleric acids in ruminal fluid decreased linearly (P < 0.05) with an increasing percentage of HSM in diet, whereas concentration of acetic acid and total volatile fatty acids in ruminal fluid tended to decrease linearly (P-value nearly 0.10) with an increasing percentage of HSM in diet. The level of blood urea nitrogen increased linearly (P < 0.05) with increasing concentration of HSM, but values were within the normal range for goats. Findings from the serum metabolite analysis and ruminal papillae morphometrics suggest that goats can be fed HSM at a concentration of up to 30% in their diet. However, growth performance results indicate that further cost-benefit analysis is required to compare HSM with other commonly used protein sources such as soybean meal. These findings will be useful for legal bodies to review during the approval process of HSM as a feed ingredient for goats in the United States.
Expert consensus recommendations on dermoscopy proficiency standards for physician assistants: results of a modified Delphi survey
Authors: Young Peter A. , Middleton Hayden T. , Griffith Cynthia F. , Froiland Christi , Keeter Nicole , Sanders Kim B. , DiRuggiero Douglas , Bae Gordon H. , Pettey Adam A. , Mostaghimi Arash , Swanson David L. , Marghoob Ashfaq A. , Nelson Kelly C. , McCleskey Patrick E. , Seiverling Elizabeth V.
Published: December 2024

Importance:

Dermoscopy is increasingly recognized by skin cancer experts and professional leaders as an essential skill for physicians in dermatology and primary care. A substantial number of patients in both settings also receive care from physician assistants (PAs), who provide additional opportunities to evaluate patients with concerning skin lesions. Earning dermatology-specific credentials from the National Commission on Certification for PAs requires passing a written exam with dermoscopic content, and 77% of practicing PAs (all specialties) believe dermoscopy should be a standard element of their formal education. No published studies have identified precise learning objectives that would represent appropriate foundational proficiency in dermoscopy for PAs.

Objective:

We sought to identify common diagnoses with distinct dermoscopic features and delineate which of these represent appropriate proficiency expectations for early-career PAs in primary care and dermatology.

Design, setting, and participants:

A panel of 14 dermoscopists was assembled (8 dermatologists; 6 PAs), reflecting contributors to existing consensus statements on physician dermoscopy proficiency benchmarks, dermatologist-recommended competencies for PAs, and/or standardized test content for dermatology PAs. Panelists completed a modified Delphi consensus process involving electronic surveys and roundtable discussions.

Main outcomes and measures:

Consensus on which specific dermoscopic diagnoses reflect appropriate foundational proficiency expectations for PAs in both primary care and dermatology.

Results:

Twelve of 14 panelists (86%) reported using dermoscopy for over 12 years (mean: 15.5 y). All panelists completed 2 iterations of an electronic survey regarding 54 diagnoses, with 39 (72%) reaching a final consensus for inclusion in PA curricula and 15 (28%) being identified as non-priority items for early-career PAs. Panelists recommended 14 conditions for primary care PAs and 25 conditions for dermatology PAs.

Conclusions and Relevance:

Consensus achieved in this modified Delphi process identified diagnoses that represent pragmatic learning objectives to achieve foundational proficiency in dermoscopy for PAs in both primary care and dermatology. This list of validated objectives provides a consensus-based guide to help educators, supervising physicians, and professional leaders to cultivate specialty-appropriate dermoscopic proficiency among early-career PAs.
SeuratIntegrate: an R package to facilitate the use of integration methods with Seurat
Authors: Specque Florian , Barré Aurélien , Nikolski Macha , Chalopin Domitille
Published: December 2024

Motivation

Integrating multiple datasets has become an increasingly common task in scRNA-seq analysis. The advent of single-cell atlases adds further complexity to this task, as they often involve combining data with complex, nested batch effects - such as those arising from multiple studies, organs or disease states. Accurate data integration is essential to distinguish cell types with sufficient granularity, thereby reflecting true biological patterns, and to create reliable reference datasets for the community. In this context, the latest version of Seurat (v5) introduced a multi-layered object structure to facilitate the integration of scRNA-seq datasets in a unified manner. However, the panel of available batch-correction methods remains limited to five algorithms within Seurat, restricting users from accessing a broader diversity of available tools, particularly Python-based methods. Furthermore, no existing R tool assists the user in making an informed decision in selecting the most appropriate integration approach.

Results

To overcome these challenges, we developed SeuratIntegrate, an open source R package that extends Seurat’s functionality. SeuratIntegrate supports eight integration methods, incorporating both R- and Python-based tools, and enables performance evaluation of integration through several scoring methods. This functionality allows for a more versatile and informed integration process.

Availability

SeuratIntegrate is available athttps://github.com/cbib/Seurat-Integrate/. The package is released under the MIT License.
Strain-based biomarkers at the skin surface differentiate asymmetries in soft tissue mobility associated with myofascial pain
Authors: Kao Anika R. , Loghmani M. Terry , Gerling Gregory J.
Published: December 2024

Objective

Soft tissue manipulation is used widely to assess myofascial tissue qualitatively but lacks objective measures. To quantify the mobility of myofascial tissue, this effort derives optical biomarkers from the skin surface, as observed in the hands-on workflow of clinicians.

Methods

Digital image correlation using three high-resolution cameras captures the cervicothoracic region as a clinician deeply engages and stretches the skin and myofascial tissue. Nineteen participants were positioned prone and marked with semi-permanent tattoos, optimized for tracking tissue without compromising its natural mechanics. Tissue mobility was then clinically assessed both bilaterally (left and right sides of body) and directionally (superior and inferior directions of pull).

Results

Eleven strain-based biomarkers were derived per tissue pull. With participants’ data aggregated, the sides of the body were indistinct, though pull in the superior direction was distinct from that in the inferior direction. Given substantial variance in the biomarkers’ absolute values between participants, we then evaluated each person individually. Therein, distinct tissue behaviors were observed. In particular, bilateral differences were identified in nine participants, eight of whom reported discrepancies in pain between their left and right sides, while directional distinctions were observed in sixteen participants, as expected given similar anatomical tissue structures between individuals.

Conclusion

In our sample of participants, optical skin surface tracking and derived strain-based biomarkers identified asymmetrical distinctions in bilateral mobility, which correspond with self-reported pain.

Significance

Such objective assessment of myofascial tissue stiffness is important in monitoring and treating chronic musculoskeletal pain, which afflicts half of the U.S. adult population.
A novel approach to identify the fingerprint of stroke gait using deep unsupervised learning
Authors: David Sina , Georgievska Sonja , Geng Cunliang , Liu Yang , Punt Michiel
Published: December 2024

Background

The gait pattern results from a complex interaction of several body parts, orchestrated by the (central) nervous system that controls the active and passive systems of the body. An impairment of gait due to a stroke results in a decline in quality of life and independence. Setting up efficient gait training requires an objective and wholesome assessment of the patient’s movement pattern to target individual gait alterations. However, current assessment tools are limited in their ability to capture the complexity of the movement and the amount of data acquired during gait analysis.

Aims

In this study, we explore the potential of variational autoencoders (VAE) to learn and recognise different gait patterns within both, pathologic and healthy gait.

Methods

For this purpose, the lower-limb joint angles of 71 participants (29 stroke survivors, 42 healthy controls) were used to train and test a VAE.

Results

The good reconstruction results (range r = 0.52 - 0.91, average normalized RMSE 23.36 % ± 4.13) indicate that VAEs extract meaningful information from the gait pattern. Furthermore, the extracted latent features are sensitive enough to distinguish between the gait patterns of stroke survivors and a healthy cohort (p<0.001).

Conclusions

The presented approach allows the assessment of gait data in an objective and wholesome manner, thereby integrating the individual characteristics of each person’s gait, making it a suitable tool for monitoring the progress of rehabilitation efforts.
Probiotics and synbiotics administered to young infants: perceptions and acceptability amongst carers and healthcare workers in Western Kenya
Authors: Otiti Mary Iwaret , Achienge Florence , Zaim Sevim , Nabwera Helen , Kariuki Simon , Allen Stephen
Published: December 2024

Background

A contributory factor to childhood undernutrition is poor gut health occurring within the first 6-12 weeks of life despite exclusive breast feeding. Pro/synbiotic administration may protect gut health. A qualitative study was conducted amongst mothers/carers and healthcare workers (HCWs) to explore their perceptions and the acceptability of pro/synbiotics administration in early life.

Methods

This study was nested within a randomised, open, clinical trial of pro/synbiotics with 32 doses administered under supervision to infants between age 0-5 months in western Kenya. Semi-structured interviews were conducted with mothers/carers, Peer Mothers and health care workers (HCWs) selected by purposive critical and key informant sampling. Interviews were transcribed and analysed using a thematic coding framework.

Findings

Satisfaction with pro/synbiotic administration was very high amongst all three groups. Commonly perceived benefits included protection from diseases, healthy growth of the infant and improved appetite. The main barriers were working mothers and other commitments making it difficult to stick to scheduled administration visits, adverse judgment and opinions in the community and lack of engagement of fathers. Insights were gained into different means of administering pro/synbiotics to young infants. Triangulation of findings of the mothers/carers with HCWs showed that most identified motivations and challenges were similar.

Conclusions

Pro/synbiotic administration was well-accepted by mothers/carers and HCWs and generally perceived to have health benefits. Administration of pro/synbiotics by mothers/carers themselves to their infants may be feasible and overcome logistical challenges. Greater efforts to sensitise and engage fathers and communities would likely be critical for a community-based program.
Ten-Second Cold Water Stress Test Differentiates Parkinson’s Disease From Multiple System Atrophy: A Pilot Study
Authors: Takahashi Makoto , Hagiwara Wataru , Itaya Sakiko , Abe Keisuke , Maeda Tetsuya , Inaba Akira , Orimo Satoshi
Published: December 2024

Background

Patients with Parkinson’s disease (PD) often have cold hands and experience frostbite. The diagnostic criteria for multiple system atrophy (MSA) also describe cold and discolored hands, but in our clinical experience we have noticed that the hands are relatively warm. These symptoms are thought to be caused by autonomic dysfunction; however, the detailed mechanisms and differences in cold hands between MSA and PD remain unclear.

Objectives

To identify an appropriate cold stimulation test to differentiate patients with PD and MSA using finger surface temperature (FST).

Methods

We included 27 and seven patients diagnosed with PD and MSA, respectively, at least 5 years after disease onset. After 15 minutes in a room with constant temperature and humidity, the patient’s hand was placed in cold water at 4°C for 10 seconds as the cold water stress test (10sec-CWST). FST was captured using a thermal imaging camera every minute for 15 minutes, and the recovery of FST was analyzed. The association between the clinical characteristics of each patient and the degree of FST recovery was examined.

Results

All patients completed the 10sec-CWST without adverse events. Patients with PD showed a significantly slower recovery of FST after 7 minutes than that of those with MSA, with a maximum difference at 11 minutes (PD: 8.1±0.6°C; MSA: 10.5±0.3°C; p<0.01). FST recovery at 11 minutes was negatively correlated with the degree of resting hand tremor (r=-0.585, p<0.01).

Conclusions

FST after 10sec-CWST may be safe and efficient test to differentiate PD and MSA.
Role of Probiotics on Dialysis Patients in End-Stage Kidney Disease: A Systematic Review
Authors: Ahmed Zaher , Karim Md. Sajjadul
Published: December 2024

The prevalence of chronic kidney disease (CKD) has been increasing all over the world due to the high-risk factors of metabolic syndrome. But, unfortunately, the cost of dialysis and the scarcity of dialysis center and dialysate are making it more complex for the people in least developed countries. Probiotics are being studied as a potential treatment option for chronic kidney disease, especially in the dialysis patients. The aim of this review is to investigate the effects of probiotics administration in dialysis patients in end-stage kidney disease. A systemic search was conducted on MEDLINE database from 2002 to 2023 using key terms related to dialysis, end-stage kidney disease and probiotics. Fifteen studies met eligibility criteria, among which thirteen were on hemodialysis patients and others on peritoneal dialysis patients. The results of the studies revealed that probiotics have some significant effect on gut dysbiosis, gastrointestinal symptoms, uremic toxins, inflammation and overall quality of life of dialytic patients. Studies showed that administration of probiotics inhibit the growth of pathogenic bacteria as well as production of protein-bound uremic toxins (i.e. indoxyl sulfate and p-cresol sulfate) which can not be fully excreted by dialysis. The level of serum TNF-α, IL-5 and IL-6 were significantly decreased in peritoneal dialysis patients. However, further investigations must be carried out with larger sample size with larger study duration and wit different probiotics or synbiotics preparations to obtained more specific explanations of the effects and mechanisms of probiotics to counteract the disease progression on dialysis patients in end-stage kidney disease.
CARS2Hypermethylation Is a Risk Factor for Stage B Heart Failure and Hospitalizations in the Project Baseline Health Study
Authors: Regan Jessica A. , Franklin Jordan , Kottilil Kalyani , Cauwenberghs Nicholas , Mahaffey Kenneth W. , Douglas Pamela S. , Rodriguez Fatima , Haddad Francois , Hernandez Adrian F. , Shah Svati H. , Kwee Lydia Coulter ,   the Project Baseline Health Study Group
Published: December 2024

The heart is a metabolically active organ with high energy demands that depend on mitochondrial oxidative phosphorylation, however as the heart begins to fail there is metabolic inflexibility and changes in mitochondrial function. Epigenetic changes such as DNA methylation can modify the transcription of genes essential for normal mitochondrial function, however this has not been studied in Stage B or pre-heart failure (HF). In 752 participants from the Project Baseline Health Study, we tested differences in DNA methylation in mitochondrial-related genes for association with Stage B HF compared to Stage A (at-risk for HF). We then validated these findings in 918 participants from the CATHGEN study for risk of incident HF hospitalization. One region on chromosome 13 overlapping with the cysteinyl-tRNA synthetase 2 (CARS2) gene, containing five cytosine-phosphate-guanine (CpG) probes, was significantly associated with a small mean regional increase in DNA methylation in Stage B HF (0.63%, Stouffer p=0.005). In CATHGEN, oneCARS2probe, cg08289839, was significantly associated with time-to-incident HF hospitalization (adjusted HR 1.74 [95% CI 1.18-2.56], FDR p=0.02). In this study of epigenetic changes of mitochondrial genes, these results indicate thatCARS2DNAm may play a role in HF pathogenesis and should be studied in future HF research.
TFClassPredict: A Novel Deep Learning Framework for Transcription Factor Binding Site Analysis Using Evolutionarily Conserved DNA-Binding Domain Annotations
Authors: Timucin Cigdem Hazal , Ickes Christian , Conrads Karly , Harms Bendix Christian , Beißbarth Tim , Haubrock Martin
Published: December 2024

Transcription factors (TFs) are proteins that regulate gene expression by binding to short specific sequences in DNA. The binding of TFs to DNA is actualized through their DNA-binding domains (DBDs). The interactions between TFs and DNA are fundamental for understanding gene regulation mechanisms, which form the basis of many cellular activities and processes. While many models have been developed to predict TF binding, there is a lack of a comprehensive model that accounts for the similarity of binding characteristics of TFs within the same DBD families. Our model, TFClassPredict, introduces a novel approach to identify transcription factor binding sites (TFBSs) based on the structural annotations of evolutionarily conserved DNA-binding domains (DBDs). By leveraging strong canonical binding patterns, TFClassPredict provides high-confidence predictions that are crucial for reliable regulatory analysis. By fine-tuning the DNABERT model, TFClassPredict was developed to classify DNA sequences across different hierarchical levels, with 6 Superclasses at the top level and 17 more specific Class-level annotations, reflecting different degrees of DBD similarity. TFClassPredict achieved high performance across both hierarchical levels, with an average AUC of 0.988, precision of 0.942, and recall of 0.906 at the SuperClass level, and an average AUC of 0.990, precision of 0.937, and recall of 0.914 at the Class-level. TFClassPredict demonstrated its ability to reveal distinct regulatory landscapes associated with cancer progression. The Class-level model is publicly available for use and can be accessed athttps://gitlab.gwdg.de/hti/tfclass_dnabert.
Inferring phenotypes of single cells based on the expression profiles of phenotype-associated marker genes in bulks and single cells
Authors: He Yin , Long Rongzhuo , Zhao Li , Wang Xiaosheng
Published: December 2024

Single-cell transcriptomes is advantageous in characterizing cell types and states, but not sufficient in describing cell phenotypes due to small cohorts in single-cell datasets. Thus, inferring single-cell phenotypes with the leverage of bulk data is practical. Here we proposed an algorithm for Single Cells’ Phenotype Prediction based on the expression profiles of phenotype-associated marker genes in bulks and single cells (ScPP). ScPP first analyzes bulk data to identify phenotype-associated marker genes. Next, ScPP evaluates the enrichment scores of the phenotype-associated marker gene sets in single cells using the AUCell algorithm. The single cells with the phenotype are defined as the intersection of the single cells with top α ranks according to the phenotype-associated AUC values and the single cells with bottom α ranks according to the opposite phenotype-associated AUC values. Finally, all single cells are determined as phenotype+, phenotype- or background. We demonstrated that ScPP could effectively recognize cell subpopulations with specific phenotypes, including tumor malignancy, estrogen receptor status, microsatellite instability, copy number variation, survival and immunotherapy response. Compared to the established algorithms (Scissor and scAB), ScPP displays more excellent predictive performance and needs less running time. Thus, ScPP is an effective and competitive tool for inferring cell phenotypes.
Thymic involution as an adaptive schedule for combating diverse pathogens
Authors: Iwasa Yoh , Matsuo Kosei
Published: December 2024

Diverse naive T cells, produced in the thymus, migrate to peripheral tissues and help suppress pathogens upon activation. As we age, the thymus shrinks, reducing both the supply and diversity of naive T cells, which increases the time required to establish immunity against new pathogens. This process, called thymic involution, is considered a form of aging. In this study, we explore whether thymic involution might be an adaptive strategy. Over time, the immune system accumulates memory cells, reducing the need for new naive T cells to combat unfamiliar pathogens. We examine how the optimal rate of naive T cell production,h(t), declines with age, taking into account the cost of maintaining thymic activity. When pathogen encounter rates are equal,h(t) decreases exponentially with age. As pathogen encounter rates rise, the initial valueh(0) increases, but the rate declines more rapidly with age, reducing overall production. A higher pathogen diversity, a greater cost of fighting new pathogens, and a lower cost of maintenance increaseh(t). When pathogen encounter rates vary,h(t) decreases with age according to a power function.

Highlights

The thymus generates diverse naive T cells to recognize a wide range of pathogens.

Thymic involution is considered an adaptive strategy, factoring in maintenance cost.

If pathogen encounters are frequent, the rate starts high but quickly declines.

The rate increases with the pathogen risk and decreases with the thymic cost.

If pathogens vary in abundances, the rate decreases as a power function of age.
A comparison study between liquid- and vapor-fed anode zero-gap bioelectrolysis cells
Authors: Rohbohm Nils , Angenent Largus T.
Published: December 2024

Improving microbial electrosynthesis could be one solution for transitioning towards sustainable chemical production, offering a pathway to convert CO2into valuable commodities from renewable energy sources. Therefore, we examined the performance differences between liquid- and vapor-fed anode zero-gap bioelectrochemical cells for electromethanogenesis, utilizing a membrane electrode assembly to enhance mass and ohmic transport. Focusing on CH4and H2production, we compared two ion-exchange membranes with the liquid-fed anode system and selected the best performing ion-exchange membrane for the vapor-fed anode system. Liquid-fed anode systems did not show significant differences in volumetric CH₄ production rates compared to vapor-fed anode systems, although the latter demonstrated advantages in reducing electrocatalyst degradation and maintaining stable cell voltages. The research underscores the need for further optimization to address performance losses and suggests potential for industrial applications of microbial electrosynthesis, highlighting the importance of catalyst protection.
Lifespan costs of reproduction increase during the Great Finnish Famine
Authors: Young Euan A. , Postma Erik , Lummaa Virpi , Dugdale Hannah L.
Published: December 2024

Evolutionary theory of aging predicts that women with increased reproductive effort live shorter lives, but evidence is inconsistent. These inconsistencies could be because environmental conditions influence how much reproductive behavior shapes a mother’s lifespan, i.e. their lifespan cost of reproduction. Using a structural equation measurement model, we compare how reproductive effort affects lifespan of 4,684 women exposed across different life-stages, or not at all, to the Great Finnish Famine. We find that lifespan costs of reproduction became higher in mothers exposed to the famine during reproduction, and for these mothers amounted to a decreased life expectancy of ~0.5 years per child. Conversely, reproductive behavior did not shape the lifespans of mothers not exposed to the famine, or exposed post-reproduction or during development. These results suggest environment-dependent reproductive costs, which provides a biological explanation for previous inconsistent findings, and demonstrate how reproductive behavior can be an important determinant of human lifespan.
Inflammatory Monocytes Increase Prior to Detectable HIV-1 Rebound Viremia
Authors: Farrell-Sherman Anna , de la Force Natalia , Prator Cecila , Valieris Renan , Azam Walker , Da Silva Israel , Deeks Steven G. , Thanh Cassandra , Bosch Ronald , Henrich Timothy J. , Cohn Lillian
Published: December 2024

The persistence of HIV-1 proviruses in latently infected cells allows viremia to resume upon treatment cessation. To characterize the resulting immune response, we compare plasma proteomics and single-cell transcriptomics of peripheral blood mononuclear cells (PBMCs) before, during, and after detectable plasma viremia. We observe unique transcriptional signatures prior to viral rebound including a significant increase in CD16++monocytes with increased anti-viral gene expression. Inflammatory proteins were identified in plasma after detectable rebound. Identifying early signals of imminent viral rebound after treatment cessation will aid in the development of strategies to prolong time to viral rebound and cure HIV-1.