Miracle-dz/UniFAR-FTUs huggingface dataset:
Effect of Purposely Induced Asymmetric Walking Perturbations on Limb Loading After Anterior Cruciate Ligament Reconstruction

Background: Patients often sustain prolonged neuromuscular dysfunction after anterior cruciate ligament reconstruction (ACLR). This dysfunction can present as interlimb loading rate asymmetries linked to reinjury and knee osteoarthritis progression. Purpose/Hypothesis: To evaluate how asymmetric walking protocols can reduce interlimb loading rate asymmetry in patients after ACLR. It was hypothesized that asymmetric walking perturbations would (1) produce a short-term adaptation of interlimb gait symmetry and (2) induce the temporary storage of these new gait patterns after the perturbations were removed. Study Design: Descriptive laboratory study. Methods: Fifteen patients who had undergone ACLR were asked to perform an asymmetric walking protocol during the study period (2022-2023). First, to classify each limb as overloaded or underloaded based on the vertical ground-reaction force loading rate for each limb, participants were asked to perform baseline symmetric walking trials. Participants then performed an asymmetric walking trial for 10 minutes, where one limb was moving 0.5 m/s faster than the other limb (1 vs 1.5 m/s), followed by a 2-minute 1 m/s symmetric deadaptation walking trial. This process was repeated with the limb speeds switched for a second asymmetric trial. Results: Participants adopted a new, symmetric interlimb loading rate gait pattern over time in response to the asymmetric trial, where the overloaded limb was set at 1 m/s. A linear mixed-effects model detected a significant change in gait dynamics (P < .001). The participants exhibited negative aftereffects after this asymmetric perturbation, indicating the temporary storage of the new gait pattern. No positive short-term gait adaptation or storage was observed when the overloaded limb was set to a faster speed. Conclusion: Asymmetric walking successfully produced the short-term adaptation of interlimb loading rate symmetry in patients after ACLR and induced the temporary storage of these gait patterns in the initial period when the perturbation was removed. Clinical Relevance: These findings are promising, as they suggest that asymmetric walking could serve as an effective gait retraining protocol that has the potential to improve long-term outcomes in patients after ACLR.
Single-cell transcriptomics reveals long noncoding RNAs associated with tumor biology and the microenvironment in pancreatic cancer

Abstract Pancreatic ductal adenocarcinoma (PDAC) is highly heterogeneous and lethal. Long noncoding RNAs (lncRNAs) are an important class of genes regulating tumorigenesis and progression. Prior bulk transcriptomic studies in PDAC have revealed the dysregulation of lncRNAs but lack single-cell resolution to distinguish lncRNAs in tumor-intrinsic biology and the tumor microenvironment (TME). We analyzed single-cell transcriptome data from 73 multiregion samples in 21 PDAC patients to evaluate lncRNAs associated with intratumoral heterogeneity and the TME in PDAC. We found 111 cell-specific lncRNAs that reflected tumor, immune and stromal cell contributions, associated with outcomes, and validated across orthogonal datasets. Single-cell analysis of tumor cells revealed lncRNAs associated with TP53 mutations and FOLFIRINOX treatment that were obscured in bulk tumor analysis. Lastly, tumor subcluster analysis revealed widespread intratumor heterogeneity and intratumoral lncRNAs associated with cancer hallmarks and tumor processes such as angiogenesis, epithelial–mesenchymal transition, metabolism and immune signaling. Intratumoral subclusters and lncRNAs were validated across six datasets and showed clinically relevant associations with patient outcomes. Our study provides the first comprehensive assessment of the lncRNA landscape in PDAC using single-cell transcriptomic data and can serve as a resource, PDACLncDB (accessible at https://www.maherlab.com/pdaclncdb-overview), to guide future functional studies.
Association of Maternal Preferred Language with Breastfeeding Attitudes, Intentions, and Knowledge

Abstract Introduction Assessing intentions, attitudes, and knowledge about breastfeeding among different language groups is important because the languages reflect cultural differences. We compared attitudes, subjective norms, perceived behavioural control, intentions, and knowledge of breastfeeding among mothers with the five most common preferred languages spoken at a New York City hospital. Materials and methods This cross-sectional study surveyed women (n = 448) in the prenatal clinic and the post-partum unit of a New York City hospital. The survey questions were about breastfeeding attitudes, subjective norms, perceived behavioural control, and intentions, based on the Theory of Planned Behavior. We also administered the Iowa Infant Feeding and Attitude Scale and measured the knowledge of the mothers about breastfeeding. The preferred language spoken by the mother was the main predictor variable. English, Russian, Spanish, Urdu, and Uzbek were the languages studied. Results Multivariate linear regression analyses showed that Russian (B = 2.24, SE = 1.09, p = 0.04), Urdu (B = 2.90, SE = 1.45, p = 0.046), and Uzbek (B = 4.21, SE = 1.35, p = 0.002) speakers all had significantly more positive attitudes toward breastfeeding than did English speakers. Spanish and English language speakers did not differ from each other in their attitudes towards breastfeeding. The language groups did not differ significantly for subjective norms, perceived behavioural control, intention to breastfeed, the Iowa Infant Feeding and Attitude Scale, nor in knowledge regarding breastfeeding. Conclusions Urdu, Uzbek, and Russian speakers had significantly more positive attitudes towards breastfeeding than did English speakers. To the extent that preferred language is a proxy for culture, clinicians can use this parameter as a basis for directing approaches toward lactation education.
The name of the game: palaeoproteomics and radiocarbon dates further refine the presence and dispersal of caprines in eastern and southern Africa

We report the first large-scale palaeoproteomics research on eastern and southern African zooarchaeological samples, thereby refining our understanding of early caprine (sheep and goat) pastoralism in Africa. Assessing caprine introductions is a complicated task because of their skeletal similarity to endemic wild bovid species and the sparse and fragmentary state of relevant archaeological remains. Palaeoproteomics has previously proved effective in clarifying species attributions in African zooarchaeological materials, but few comparative protein sequences of wild bovid species have been available. Using newly generated type I collagen sequences for wild species, as well as previously published sequences, we assess species attributions for elements originally identified as caprine or ‘unidentifiable bovid’ from 17 eastern and southern African sites that span seven millennia. We identified over 70% of the archaeological remains and the direct radiocarbon dating of domesticate specimens allows refinement of the chronology of caprine presence in both African regions. These results thus confirm earlier occurrences in eastern Africa and the systematic association of domesticated caprines with wild bovids at all archaeological sites. The combined biomolecular approach highlights repeatability and accuracy of the methods for conclusive contribution in species attribution of archaeological remains in dry African environments.
Reconstructing the feeding ecology of Cambrian sponge reefs: the case for active suspension feeding in Archaeocyatha

Sponge-grade Archaeocyatha were early Cambrian biomineralizing metazoans that constructed reefs globally. Despite decades of research, many facets of archaeocyath palaeobiology remain unclear, making it difficult to reconstruct the palaeoecology of Cambrian reef ecosystems. Of specific interest is how these organisms fed; previous experimental studies have suggested that archaeocyaths functioned as passive suspension feeders relying on ambient currents to transport nutrient-rich water into their central cavities. Here, we test this hypothesis using computational fluid dynamics (CFD) simulations of digital models of select archaeocyath species. Our results demonstrate that, given a range of plausible current velocities, there was very little fluid circulation through the skeleton, suggesting obligate passive suspension feeding was unlikely. Comparing our simulation data with exhalent velocities collected from extant sponges, we infer an active suspension feeding lifestyle for archaeocyaths. The combination of active suspension feeding and biomineralization in Archaeocyatha may have facilitated the creation of modern metazoan reef ecosystems.
Bacillus‐based probiotic cleansers reduce the formation of dry biofilms on common hospital surfaces

In the absence of liquid suspension, dry biofilms can form upon hard surfaces within a hospital environment, representing a healthcare‐associated infection risk. Probiotic cleansers using generally recognized as safe organisms, such as those of the Bacillus genus, represent a potential strategy for the reduction of dry biofilm bioburden. The mechanisms of action and efficacy of these cleaners are, however, poorly understood. To address this, a preventative dry biofilm assay was developed using steel, melamine, and ceramic surfaces to assess the ability of a commercially available Bacillus spp. based probiotic cleanser to reduce the surface bioburden of Escherichia coli and Staphylococcus aureus. Via this assay, phosphate‐buffered saline controls were able to generate dry biofilms within 7 days of incubation, with the application of the probiotic cleanser able to prevent >97.7% of dry biofilm formation across both pathogen analogs and surface types. Further to this, surfaces treated with the probiotic mixture alone also showed a reduction in dry biofilm across both pathogen and surface types. Confocal laser scanning microscopy imaging indicated that the probiotic bacteria were able to germinate and colonize surfaces, likely forming a protective layer upon these hard surfaces.
Sublethal doses of insecticide reduce thermal tolerance of a stingless bee and are not avoided in a resource choice test

Insecticides and climate change are among the multiple stressors that bees face, but little is known about their synergistic effects, especially for non-Apis bee species. In laboratory experiments, we tested whether the stingless bee Tetragonula hockingsi avoids insecticide in sucrose solutions and how T. hockingsi responds to insecticide and heat stress combined. We found that T. hockingsi neither preferred nor avoided sucrose solutions with either low (2.5 × 10−4 ng µl−1 imidacloprid or 1.0 × 10−4 ng µl−1 fipronil) or high (2.5 × 10−3 ng µl−1 imidacloprid or 1.0 × 10−3 ng µl−1 fipronil) insecticide concentrations when offered alongside sucrose without insecticide. In our combined stress experiment, the smallest dose of imidacloprid (7.5 × 10−4 ng) did not significantly affect thermal tolerance (CTmax). However, CTmax significantly reduced by 0.8°C (±0.16 SE) and by 0.5°C (±0.16 SE) when bees were fed as little as 7.5 × 10−3 ng of imidacloprid or 3.0 × 10−4 ng of fipronil, respectively, and as much as 1.5°C (±0.16 SE) and 1.2°C (±0.16 SE) when bees were fed 7.5 × 10−2 ng of imidacloprid or 3.0 × 10−2 ng of fipronil, respectively. Predictions of temperature increase, and increased insecticide use in the tropics suggest that T. hockingsi will be at increased risk of the effects of both stressors in the future.
Assessment of four in vitro phenotypic biofilm detection methods in relation to antimicrobial resistance in aerobic clinical bacterial isolates

Introduction The lack of standardized methods for detecting biofilms continues to pose a challenge to microbiological diagnostics since biofilm-mediated infections induce persistent and recurrent infections in humans that often defy treatment with common antibiotics. This study aimed to evaluate diagnostic parameters of four in vitro phenotypic biofilm detection assays in relation to antimicrobial resistance in aerobic clinical bacterial isolates. Methods In this cross-sectional study, bacterial strains from clinical samples were isolated and identified following the standard microbiological guidelines. The antibiotic resistance profile was assessed through the Kirby-Bauer disc diffusion method. Biofilm formation was detected by gold standard tissue culture plate method (TCPM), tube method (TM), Congo red agar (CRA), and modified Congo red agar (MCRA). Statistical analyses were performed using SPSS version 17.0, with a significant association considered at p<0.05. Result Among the total isolates (n = 226), TCPM detected 140 (61.95%) biofilm producers, with CoNS (9/9) (p<0.001) as the predominant biofilm former. When compared to TCPM, TM (n = 119) (p<0.001) showed 90.8% sensitivity and 70.1% specificity, CRA (n = 88) (p = 0.123) showed 68.2% sensitivity and 42% specificity, and MCRA (n = 86) (p = 0.442) showed 65.1% sensitivity and 40% specificity. Juxtaposed to CRA, colonies formed on MCRA developed more intense black pigmentation from 24 to 96 hours. There were 77 multi-drug-resistant (MDR)-biofilm formers and 39 extensively drug-resistant (XDR)-biofilm formers, with 100% resistance to ampicillin and ceftazidime, respectively. Conclusion It is suggested that TM be used for biofilm detection, after TCPM. Unlike MCRA, black pigmentation in colonies formed on CRA declined with time. MDR- and XDR-biofilm formers were frequent among the clinical isolates.
Reinforcing the idea of an early dispersal of Hippopotamus amphibius in Europe: Restoration and multidisciplinary study of the skull from the Middle Pleistocene of Cava Montanari (Rome, central Italy)

A skull of Hippopotamus recovered from the area of Tor di Quinto, within the urban area of Rome (central Italy) is here redescribed. Despite being one of the most complete specimens of hippopotamuses of the European Pleistocene, the Tor di Quinto skull did not attract much research interest, due to long-standing uncertainties on its provenance. This work begun in 2021, when the skull was restored, within a large renovation project on the vertebrate exposed at the Earth Science University Museum of Sapienza University of Rome. Original sediments were found inside the cranial and mandible cavities during the restoration work, which were sampled for petrographic analyses. By combining a review of the old paleontological, archeological and geological literature published during the 19th and 20th century on the Rome basin and the correlation of these new sedimentological and petrographic information with the lithostratigraphic and synthemic units of the national geological cartography, we clarify that the Hippopotamus skull was most likely to have been collected from a quarry called Cava Montanari, from a formation dated between 560 and 460 ka. Morphological and biometric analyses clearly support an attribution of the Cava Montanari specimen to the extant species Hippopotamus amphibius. The reassessment of the stratigraphic and geological data on Cava Montanari implies that the studied specimen is the earliest confirmed occurrence of Hippopotamus amphibius in the European fossil record.
Population dynamics of northern bobwhites in southern Texas

Population Dynamics of Northern Bobwhites in Southern Texas. (December 2008) Stephen J. DeMaso, B.S., Michigan State University; M.S., Texas A&M University–Kingsville Co-Chairs of Advisory Committee: Dr. Fidel Hernandez Dr. Nova J. Silvy Northern bobwhites (Colinus virginianus) are an important cultural, ecological, and economical part of the southern Texas landscape. I used radio-telemetry data from 2000–2005, part of a long-term, bobwhite study in southern Texas, to test the nestconcealment hypothesis, develop a stochastic simulation model for bobwhite populations, and evaluate the influence of brush canopy coverage (BCC) on shortand long-term demographic performance of bobwhites. Bobwhite nests tend to be situated in taller and denser vegetation than would be expected if nest-site location was a random process. I compared 4 microhabitat variables between successful (n = 135) and depredated nests (n = 118). I documented similar microhabitat attributes between successful and depredated nests. The discriminant function correctly classified only 48–59% of nest fates into the correct group, but only 18% of the variation in nest fate. Thus, my results did not support the nest-concealment hypothesis. My stochastic simulation model for bobwhite populations is based on difference equations (Δt = 3 months) and simulations run for 100 years using STELLA 9.0. 2. The
Baseline characteristics and the factors influencing successful smoking cessation: A comparison between a WeChat smoking cessation mini-program and an offline smoking cessation clinic

INTRODUCTION Smoking cessation (SC) clinics are a professional SC services in China. However, studies comparing the characteristics and SC rates of smoking populations in SC clinics with those using mobile SC programs are limited. We compared smokers’ characteristics, 3-month SC rates, and the factors influencing 3-month SC success, between a large hospital SC clinic and a WeChat SC mini-program. METHODS Between January and November 2021, 384 participants voluntarily enrolled in either the hospital SC clinic (Group A: n=243) or the WeChat SC mini-program (Group B: n=141). Both groups underwent a 3-month SC intervention, and their SC status was monitored at 24 hours, 1 week, 1 month, and 3 months after quitting. SC rate was defined as the self-reported rate of continuous SC. RESULTS The 3-month SC rate was higher in Group A (42.4%) than in Group B (24.8%). Participants with middle school education had a lower likelihood of SC success than those with primary school or lower (p=0.014). Employees in the enterprise/business/services industries were more likely to have SC success than farmers (p=0.013). Participants with SC difficulty scores of 0–60 were more successful than those with scores >60 (p=0.001, p=0.000, respectively). Participants who quit smoking due to their illness, or other reasons, had a higher likelihood of SC success than those who quit due to concerns about their own and their family's health (p=0.006, p=0.098, respectively). While the likelihood of SC success was lower in those who quit because of the influence of their environment than in those who quit due to concerns about their own and their family's health (p=0.057). CONCLUSIONS Both SC clinics and WeChat SC mini-programs achieved satisfactory SC rates. The high accessibility of mobile SC platforms, which save time spent on transportation and medical visits, renders them worth promoting and publicizing as additional SC options for smokers, particularly young smokers.
Regional White Matter Hyperintensities Relate to Specific Cognitive Abilities in Older Adults Without Dementia

Introduction: White matter hyperintensities (WMHs) are magnetic resonance imaging markers of small vessel cerebrovascular disease that are associated with cognitive decline and clinical Alzheimer disease. Previous studies have often focused on global or total WMH; less is known about associations of regional WMHs and cognitive abilities among older adults without dementia. Methods: A total of 610 older adults with normal cognition (n=302) or mild cognitive impairment (n=308) from the Alzheimer’s Disease Neuroimaging Initiative underwent neuropsychological testing and magnetic resonance imaging. Linear regression models examined associations between regional WMH volumes and cognition, adjusting for age, sex, education, apolipoprotein E ε4 allele frequency, and pulse pressure. Results: Among all participants, greater regional WMH volume in all lobes was associated with poorer performance on memory and speed/executive functioning. Among participants with normal cognition, greater temporal and occipital WMH volumes were associated with poorer memory, whereas no regional WMH volumes were associated with speed/executive function. Discussion: Results show that greater regional WMH volume relates to poorer cognitive functioning—even among those with normal cognition. Together with results from previous studies, our findings raise the possibility that WMH may be a useful therapeutic target and/or important effect modifier in treatment or prevention dementia trials.
Suicidal ideation, plan, and attempt among men who have sex with men in Nepal: Findings from a cross-sectional study

Men who have sex with men (MSM) are at increased risk for suicide, with a much higher prevalence of suicidality than the general population. While there is a growing interest in the identification of risk factors for suicidal behaviors globally, the understanding of the prevalence and risk factors for suicidal behaviors among MSM in the context of low- and middle-income countries is almost non-existent. Therefore, this study aimed to investigate suicidal ideation, plan, and attempts, and related factors among MSM in Nepal. A cross-sectional respondent driven survey was conducted on 250 MSM between October and December 2022. Bivariate and multivariable logistic regression was used to evaluate independent correlates of suicidal behaviors of MSM. Overall, the lifetime prevalence of suicidal ideation, plans, and attempts among MSM in this study were 42.4%, 31.2%, and 21.6%, respectively. MSM with depressive symptoms (aOR = 5.7, 95% CI = 2.4–14.1), advanced education (higher secondary and above; aOR = 2.9, 95% CI = 1.4–6.1), and smoking habit (aOR = 2.5, 95% CI = 1.2–5.3) were at increased risk for suicidal ideation. Similarly, those with depressive symptoms (aOR = 2.2, 95% CI = 1.1–4.8) and advanced education (aOR = 2.7, 95% CI = 1.2–5.7) were more likely to plan suicide, whereas young MSM were significantly more prone to attempting suicide (aOR = 2.7, 95% CI = 1.3–5.8). Interestingly, MSM with moderate to severe food insecurity were 2–3 times more likely to think about, plan, or attempt suicide (ideation: aOR = 3.5, 95% CI = 1.6–7.7; plan: aOR = 3.7, 95% CI = 1.6–8.3; attempt: aOR = 2.2, 95% CI = 1.1–4.6). The results suggest the importance of early assessment of suicidal behaviors among MSM and the need for tailored interventions to simultaneously address mental health problems and food insecurity to reduce suicide-related problems among Nepalese MSM.
A new approach to derive productivity of tropical forests using radar remote sensing measurements

Deriving gross & net primary productivity (GPP & NPP) and carbon turnover time of forests from remote sensing remains challenging. This study presents a novel approach to estimate forest productivity by combining radar remote sensing measurements, machine learning and an individual-based forest model. In this study, we analyse the role of different spatial resolutions on predictions in the context of the Radar BIOMASS mission (by ESA). In our analysis, we use the forest gap model FORMIND in combination with a boosted regression tree (BRT) to explore how spatial biomass distributions can be used to predict GPP, NPP and carbon turnover time (τ) at different resolutions. We simulate different spatial biomass resolutions (4 ha, 1 ha and 0.04 ha) in combination with different vertical resolutions (20, 10 and 2 m). Additionally, we analysed the robustness of this approach and applied it to disturbed and mature forests. Disturbed forests have a strong influence on the predictions which leads to high correlations (R2 > 0.8) at the spatial scale of 4 ha and 1 ha. Increased vertical resolution leads generally to better predictions for productivity (GPP & NPP). Increasing spatial resolution leads to better predictions for mature forests and lower correlations for disturbed forests. Our results emphasize the value of the forthcoming BIOMASS satellite mission and highlight the potential of deriving estimates for forest productivity from information on forest structure. If applied to more and larger areas, the approach might ultimately contribute to a better understanding of forest ecosystems.