Miracle-dz/UniFAR-FTUs huggingface dataset:
The elite common bean Phaseolus vulgaris cultivar Pinto Saltillo hosts a rich and diverse array of plant-growth promoting bacteria in its rhizosphere

The rhizosphere of crop plants is a nutrient-rich niche that is inhabited by many microorganisms. Root-associated microorganisms play a crucial role in crop yields in agriculture. Given the ample diversity of varieties and cultivars of the common bean (Phaseolus vulgaris) used in agriculture, it is important to characterize their bacterial communities. In this study, we analyzed the bacterial rhizosphere components of the bean cultivar Pinto Saltillo, which is widely produced and consumed in Mexico. Bulk soil and rhizosphere samples from the P. vulgaris cultivar Pinto Saltillo were collected in situ from plots with and without cultivation history. Metagenomic analysis revealed that in both plots, the bacterial diversity in the bulk soil exceeded that in the rhizosphere. Moreover, diversity and taxonomic composition analysis confirmed the dominance of Proteobacteria in the rhizosphere. Comparisons with pairs of bulk soil-rhizosphere metagenomes of other cultivated plants (maize, wheat, tomato, cucumber, and the model plant Arabidopsis) indicated a pronounced rhizosphere effect of the cultivar Pinto Saltillo, particularly regarding the presence of bacterial genera already known as plant growth promoters, including Rhizobium. Metagenome-assembled genomes (MAGs) reconstructed from metagenomes confirmed a diverse set of species at the OTU level, closely related to this group of microorganisms. Our analysis underscores the association of R. sophoriradicis strains as the primary nodulating agent of common beans in the sampled agricultural fields. These findings imply that the success of common bean crops relies on microbial species that are still inadequately characterized beyond the established role of nitrogen-fixing bacteria. Importance Sustainable agriculture is a long-term goal aimed at mitigating the impact of modern intensive and polluting agricultural technologies. Significant efforts are underway to understand the contributions of microorganisms to the health and productivity of crop plants. The common bean (Phaseolus vulgaris) is a domesticated leguminous plant native to Mesoamerica, that whose seeds provide sustenance for millions of people in America and Africa. Previous studies have illuminated the bacterial diversity of the rhizosphere microbiome in relation to plant resistance to pathogens and in the domestication process. These findings underscore the importance of investigating the bacterial rhizosphere communities in successful cultivars of the common bean. In this study, we demonstrate that the common bean cultivar Pinto Saltillo hosts a diverse array of plant-growth promoting bacteria in its rhizosphere. These findings suggest that the agricultural success of common bean cultivars could be attributed to the interplay between the plant and its rhizosphere bacterial community, rather than solely relying on nitrogen-fixing symbiosis.
Light-driven synchronization of optogenetic clocks

Synthetic genetic oscillators can serve as internal clocks within engineered cells to program periodic expression. However, cell-to-cell variability introduces a dispersion in the characteristics of these clocks that drives the population to complete desynchronization. Here we introduce the optorepressilator, an optically controllable genetic clock that combines the repressilator, a three-node synthetic network in E. coli, with an optogenetic module enabling to reset, delay, or advance its phase using optical inputs. We demonstrate that a population of optorepressilators can be synchronized by transient green light exposure or entrained to oscillate indefinitely by a train of short pulses, through a mechanism reminiscent of natural circadian clocks. Furthermore, we investigate the system’s response to detuned external stimuli observing multiple regimes of global synchronization. Integrating experiments and mathematical modeling, we show that the entrainment mechanism is robust and can be understood quantitatively from single cell to population level.
Roles of SNORD115 and SNORD116 ncRNA clusters in neuronal differentiation

Prader-Willi syndrome shows features linked to brain development and hypothalamus-related endocrine abnormalities. The smallest clinical deletions fall within the large (∼650Kb) SNHG14 gene, removing 29 consecutive introns that each generate SNORD116. SNHG14 also includes 48 tandem introns encoding SNORD115 and generates multiple, extended snoRNA-related species. SNORD115 and SNORD116 resemble box C/D small nucleolar RNAs (snoRNAs) but lack known targets. Both snoRNAs strongly accumulated during neuronal differentiation. SNORD116 accumulation apparently reflected stabilization, potentially linked to the appearance of FBLL1, a homologue of the ubiquitous snoRNA-associated protein Fibrillarin (FBL). In contrast, SNORD115 was selectively transcribed, apparently due to regulated termination. For functional characterization we created cell lines lacking only the expressed, paternal, SNORD115 or SNORD116 cluster. Analyses during neuronal development indicated changes in RNA stability and protein synthesis. Altered mRNAs included MAGEL2, mutation of which causes the PWS-like disorder Schaaf-Yang syndrome. Comparison of SNORD115 and SNORD116 mutants indicated overlapping or interacting functions. Most changes in mRNA and protein abundance appeared relatively late in development, with roles including cytoskeleton formation, extracellular matrix, neuronal arborization. Comparison with human embryonic midbrain development suggested enhanced progression in neuronal development in the snoRNA mutants. Subtle impairment of relative neuronal maturation during development, might generate the clinical phenotypes.
Optical Genome Mapping for Oncology Applications

Optical genome mapping (OGM) is a next‐generation cytogenomic technology that has the potential to replace standard‐of‐care technologies used in the genetic workup of various malignancies. The ability to detect various classes of structural variations that include copy number variations, deletions, duplications, balanced and unbalanced events (insertions, inversions, and translocation) and complex genomic rearrangements in a single assay and analysis demonstrates the utility of the technology in tumor research and clinical application. Herein, we provide the methodological details for performing OGM and pre‐ and post‐analytical quality control (QC) checks and describe critical steps that should be performed with caution, probable causes for specific QC failures, and potential method modifications that could be implemented as part of troubleshooting. The protocol description and troubleshooting guide should help new and current users of the technology to improve or troubleshoot the problems (if any) in their workflow. © 2023 Wiley Periodicals LLC.
Outcomes of Sling Procedure Using a Free Vascularized Fibular Graft After Resection of the Proximal Humerus

Background: The proximal humerus is a common site for both primary and metastatic bone tumors. Although various methods have been developed for reconstruction following resection of the proximal humerus, a consensus on which technique is best has not been established. We focused on the sling procedure using a free vascularized fibular graft (FVFG) and conducted what we believe to be the largest retrospective study of patients to undergo this surgery to date. Methods: We retrospectively reviewed the data of 19 patients who underwent the sling procedure with use of an FVFG at our hospital between 1998 and 2022. The median age was 20 years, and the median follow-up duration was 63.1 months. Surgical data, oncological outcomes, the postoperative course, complications, and functional outcomes as measured with use of the Musculoskeletal Tumor Society (MSTS) score were thoroughly reviewed. Results: The median operative duration was 555 minutes, and the median blood loss was 374 mL. The median length of the bone defect was 17.0 cm, and the median length of the graft was 20.0 cm. With respect to oncological outcomes, 9 patients were continuously disease-free, 9 patients had no evidence of disease, and 1 patient was alive with disease. Bone union was present in 13 of the 17 patients for whom it was evaluable. The median time to bone union was 4 months. Graft growth was observed in 2 pediatric patients. Postoperative fracture was a major complication at the recipient site. The incidence of pseudarthrosis significantly increased when the FVFG could not be inserted into the remaining humeral bone or was split in half (p = 0.002). Although a few patients demonstrated peroneal nerve palsy at the donor site, the symptom was temporary. The overall functional outcome was favorable, with an average MSTS score of 66.9%. Conclusions: The sling procedure demonstrated a low complication rate and a favorable functional outcome overall. Therefore, we believe that this procedure is a useful reconstruction method for patients in a broad age range who have a wide defect of the proximal humerus. Level of Evidence: Therapeutic Level IV. See Instructions for Authors for a complete description of levels of evidence.
On the Equivalence of Two Conceptual Models for Describing Ion Exchange During Transport Through an Aggregated Oxisol

Breakthrough curves (BTCs) of the cation 45Ca2+, an anion 36Cl−, and 3H2O were measured during miscible displacement through water-saturated soil columns packed with aggregates of an Oxisol. Two conceptual models were used to simulate the observed asymmetry and tailing in the BTCs caused by an apparent nonequilibrium situation in the porous medium. In both models the exchange process on one type of site was assumed to be instantaneous while the rate of isotopic exchange on another type of site was assumed to be either a diffusion-controlled process (model 1) or a first-order reversible kinetic process (model 2). Isotopic exchange in both models was described with a linear isotherm. It is shown that the two models are mathematically equivalent with respect to the derived BTCs.
Snacks contribute considerably to total dietary intakes among adults stratified by glycemia in the United States

Little is known about the snacking patterns among adults with type 2 diabetes. The contribution of snacks to energy and nutrient intakes is important to further understand dietary patterns and glycemic control. The purpose of this study is to evaluate snack consumption among adults according to diabetes status in the United States. One NHANES 24-hour dietary recall for each participant collected between 2005–2016 was utilized for analysis (n = 23,708). Analysis of covariance was used to compare differences in nutrient and food groups intakes from snacks across levels of glycemic control, while controlling for age, race/ethnicity, income, marital status, and gender. Results of this analysis inform that adults with type 2 diabetes consume less energy, carbohydrates, and total sugars from snacks than adults without diabetes. Those with controlled type 2 diabetes consumed more vegetables and less fruit juice than other groups, yet adults with type 2 diabetes in general consumed more cured and luncheon meats than adults without diabetes or with prediabetes. Protein from all snacks for those without diabetes is higher than all other groups. This study elucidates common snacking patterns among US adults with diabetes and highlights the need for clinicians and policymakers to take snacking into consideration when evaluating and providing dietary recommendations.
Ancient origin of the rod bipolar cell pathway in the vertebrate retina

Vertebrates rely on rod photoreceptors for vision in low-light conditions. Mammals have a specialized downstream circuit for rod signaling called the primary rod pathway, which comprises specific cell types and wiring patterns that are thought to be unique to this lineage. Thus, it has been long assumed that the primary rod pathway evolved in mammals. Here, we challenge this view by demonstrating that the mammalian primary rod pathway is conserved in zebrafish, which diverged from extant mammals ~400 million years ago. Using single-cell RNA-sequencing, we identified two bipolar cell (BC) types in zebrafish that are related to mammalian rod BCs (RBCs) of the primary rod pathway. By combining electrophysiology, histology, and ultrastructural reconstruction of the zebrafish RBCs, we found that, like mammalian RBCs, both zebrafish RBC types connect with all rods in their dendritic territory, and provide output largely onto amacrine cells. The wiring pattern of the amacrine cells post-synaptic to one RBC type is strikingly similar to that of mammalian RBCs, suggesting that the cell types and circuit design of the primary rod pathway have emerged before the divergence of teleost fish and amniotes. The second RBC type, which forms separate pathways, is either lost in mammals or emerged in fish.
Quantification of Surgical Workflow during Robotic Proctectomy

Aim: Assessments of surgical workflow offer insight regarding procedure variability, case complexity and surgeon proficiency. We utilize an objective method to evaluate step-by-step workflow and step transitions during robotic proctectomy (RP). Methods: We annotated 31 RPs using a procedure-specific annotation card. Using Spearman’s correlation, we measured strength of association of step time and step visit frequency with console time (CT) and total operative time (TOT). Results: Across 31 RPs, a mean (± standard deviation) of 49.0 (± 20.3) steps occurred per procedure. Mean CT and TOT were 213 (± 90) and 283 (± 108) minutes. Posterior mesorectal dissection required most visits (8.7 ± 5.0), while anastomosis required most time (18.0 [± 8.5] minutes). Inferior mesenteric vein (IMV) ligation required least visits (1.0 ± 0.0) and lowest duration (0.9 [± 0.5] minutes). Strong correlations were seen with CT and step times for IMV dissection and ligation (ρ = 0.60 for both), lateral-to-medial splenic flexure mobilization (SFM) (ρ = 0.63), left rectal dissection (ρ = 0.64) and mesorectal division (ρ = 0.71). CT correlated strongly with medial-to-lateral and supracolic SFM visit frequency (ρ = 0.75 and ρ = 0.65). There were strong correlations with TOT and initial exposure time (ρ = 0.60), as well as visit frequency for medial-to-lateral (ρ = 0.67) and supracolic SFM (ρ = 0.65). Descending colon mobilization was nodal, rectal mobilization convergent and rectal transection divergent. Conclusion: This study correlates individual surgical steps with CT and TOT through standardized annotation. It provides an objective approach to quantify workflow.
A machine learning approach for computation of cardiovascular intrinsic frequencies

Analysis of cardiovascular waveforms provides valuable clinical information about the state of health and disease. The intrinsic frequency (IF) method is a recently introduced framework that uses a single arterial pressure waveform to extract physiologically relevant information about the cardiovascular system. The clinical usefulness and physiological accuracy of the IF method have been well-established via several preclinical and clinical studies. However, the computational complexity of the current L2 optimization solver for IF calculations remains a bottleneck for practical deployment of the IF method in real-time settings. In this paper, we propose a machine learning (ML)-based methodology for determination of IF parameters from a single carotid waveform. We use a sequentially-reduced Feedforward Neural Network (FNN) model for mapping carotid waveforms to the output parameters of the IF method, thereby avoiding the non-convex L2 minimization problem arising from the conventional IF approach. Our methodology also includes procedures for data pre-processing, model training, and model evaluation. In our model development, we used both clinical and synthetic waveforms. Our clinical database is composed of carotid waveforms from two different sources: the Huntington Medical Research Institutes (HMRI) iPhone Heart Study and the Framingham Heart Study (FHS). In the HMRI and FHS clinical studies, various device platforms such as piezoelectric tonometry, optical tonometry (Vivio), and an iPhone camera were used to measure arterial waveforms. Our blind clinical test shows very strong correlations between IF parameters computed from the FNN-based method and those computed from the standard L2 optimization-based method (i.e., R≥0.93 and P-value ≤0.005 for each IF parameter). Our results also demonstrate that the performance of the FNN-based IF model introduced in this work is independent of measurement apparatus and of device sampling rate.
Attitudes, Practices and Understanding of health workers and caregivers regarding the relationship between severe pneumonia and malnutrition in children: A Qualitative Study

Abstract Background Severe Pneumonia is still the leading cause of morbidity and mortality among children worldwide. Many children with severe pneumonia are reported to die in hospital as well as following discharge due to malnutrition. Severe pneumonia is a catabolic illness, which predisposes to severe malnutrition. WHO and United Nations Children’s Fund (UNICEF), recommend ‘continued’ feeding but do not give any specific recommendations for nutritional support. This could influence health workers’ and caregivers’ attitudes, practices and understanding regarding the topic. This study aimed to explore the attitudes, practices and understanding of health workers regarding the relationship between severe pneumonia and malnutrition. Methods We conducted an exploratory qualitative study among health workers and caregivers of children hospitalized with severe pneumonia at Mulago National Referral Hospital in Uganda. Data were collected using focus-groups involving caregivers and key informant interviews with health workers and analysed using the content-thematic analysis approach. Both manual coding and Atlas Ti software were used to support the analysis. Results Some of the health workers and caregivers were aware of the relationship between severe pneumonia and malnutrition to various degrees, citing reduced appetite, difficulty in breathing and persistent vomiting as pathways to malnutrition in patients with severe pneumonia, which called for a balanced diet and more frequent breastfeeding. Suppressed immunity in malnourished children was mentioned as the pathway to severe pneumonia. Some caregivers confessed not knowing anything about the relationship between the two conditions. Conclusion Attitudes, practices and understanding regarding the deadly relationship between severe pneumonia and malnutrition among care givers could further be improved by health education and mass sensitization. Clarifying practice guidelines could further enhance attitudes and practices of health workers to reduce preventable pneumonia deaths.
Measuring novice-expert sense of place for a far-away place: Implications for geoscience instruction

Individuals usually develop a sense of place through lived experiences or travel. Here we introduce new and innovative tools to measure sense of place for remote, far-away locations, such as Greenland. We apply this methodology within place-based education to study whether we can distinguish a sense of place between those who have visited Greenland or are otherwise strongly connected to the place from those who never visited. Place-based education research indicates that an increased sense of place has a positive effect on learning outcomes. Thus, we hypothesize that vicarious experiences with a place result in a measurably stronger sense of place when compared to the sense of place of those who have not experienced the place directly. We studied two distinct groups; the first are people with a strong Greenland connection (experts, n = 93). The second are students who have never been there (novices, n = 142). Using i) emotional value attribution of words, ii) thematic analysis of phrases and iii) categorization of words, we show significant differences between novice’s and expert’s use of words and phrases to describe Greenland as a proxy of sense of place. Emotional value of words revealed statistically significant differences between experts and novices such as word power (dominance), feeling pleasantness (valence), and degree of arousal evoked by the word. While both groups have an overall positive impression of Greenland, 31% of novices express a neutral view with little to no awareness of Greenland (experts 4% neutral). We found differences between experts and novices along dimensions such as natural features; cultural attributes; people of Greenland; concerns, importance, or interest in and feeling connected to Greenland. Experts exhibit more complex place attributes, frequently using emotional words, while novices present a superficial picture of Greenland. Engaging with virtual environments may shift novice learners to a more expert-like sense of place, for a far-away places like Greenland, thus, we suggest virtual field trips can supplement geoscience teaching of concepts in far-away places like Greenland and beyond.
How do industry and province attributes impact corporate contribution to poverty alleviation: A multilevel analysis

This study employs a multilevel model, nesting firm observations within industry and province groups, to investigate the influences on corporate contributions to poverty alleviation while considering the industrial and provincial contexts. Using a sample of Chinese firms listed in Shanghai and Shenzhen Stock Exchanges between 2016 and 2019, we find that Herfindah-Hirschman Index (HHI) does not affect corporate contribution. The results show a significantly negative relationship between industry dynamism and a firm’s substantial poverty contributions, as well as a significantly positive relationship between number of state-owned enterprises (SOEs) in industry and the likelihood and extent of a firm’s contributions. Moreover, a firm’s likelihood to participate in anti-poverty activities and make substantial contributions is affected by more intense government intervention and lower per capita GDP. A province’s poverty rate is positively associated with the extent of corporate investments in poverty alleviation. Additional analyses note that firms competitive in an industry that is less dynamic environment are more likely to invest funds into poverty alleviation instead of material contribution. Moreover, for firms headquartered in an industry with more SOEs and in provinces with a stronger government, a higher poverty rate and lower per capita GDP mean it is more likely for them to make both monetary and material contributions for anti-poverty campaigns.