Miracle-dz/UniFAR-FTUs huggingface dataset:
Revisiting the oldest manure of India, Kunapajala: Assessment of its animal waste recycling potential as a source of plant biostimulant

India's oldest documented manure, most commonly referred to as Kunapajala, has a long history of over 1,000 years in crop cultivation. Kunapajala is primarily an in-situ decomposition technology of animal waste and can potentially provide an eco-friendly pipeline for recycling bio-waste into essential plant nutrients. This traditional animal manure, in addition, also contains dairy excreta (e.g., feces and urine), dairy products (e.g., milk and ghee), natural resources (e.g., honey), broken seeds or grains, and their non-edible by-product waste. Here, we aimed to assess the waste recycling and plant biostimulant potential of Kunapajala prepared from livestock (e.g., Black Bengal goats) or fish (e.g., Bombay duck) post-processed wastes over different decomposition periods, e.g., (0, 30, 60, and 90-days). In this study, an in-situ quantification of livestock- (lKPJ) and fish-based Kunapajala (fKPJ) reveals a dynamic landscape of essential plant primary nutrients, e.g., (0.70 > NH4-N < 3.40 g•L−1), (100.00 > P2O5 < 620.00 mg•L−1), and (175.00 > K2O < 340.00 mg•L−1), including other physico-chemical attributes of Kunapajala. Using correlation statistics, we find that the plant-available nutrient content of Kunapajala depicts a significant (p < 0.0001) transformation over decomposition along with microbial dynamics, abundance, and diversities, delineating a microbial interface to animal waste decomposition and plant growth promotion. Importantly, this study also reports the indole 3-acetic acid (IAA) content (40.00 > IAA < 135.00 mg•L−1) in Kunapajala. Furthermore, the bacterial screening based on plant growth-promoting traits and their functional analyses elucidate the mechanism of the plant biostimulant potential of Kunapajala. This assay finally reports two best-performing plant growth-promoting bacteria (e.g., Pseudomonas chlororaphis and Bacillus subtilis) by the 16S ribotyping method. In support, in-planta experiments have demonstrated, in detail, the bio-stimulative effects of Kunapajala, including these two bacterial isolates alone or in combination, on seed germination, root-shoot length, and other important agronomic, physio-biochemical traits in rice. Together, our findings establish that Kunapajala can be recommended as a source of plant biostimulant to improve crop quality traits in rice. Overall, this work highlights Kunapajala, for the first time, as a promising low-cost microbial technology that can serve a dual function of animal waste recycling and plant nutrient recovery to promote sustainable intensification in agroecosystems.
Phenotypic and genetic parameters of circadian rhythms from core body temperature profiles and their relationships with beef steers’ production efficiency profiles during successive winter feeding periods

This 2-year study evaluated differences in circadian parameters obtained from measures of core body temperatures using telemetric reticulo-rumen and rectal devices during two winter feeding regimes in western Canada. The study also estimated phenotypic correlations and genetic parameters associated with circadian parameters and other production traits in each feeding regime. Each year, 80 weaned steer calves (initial age: 209 ± 11 days; BW: 264 ± 20 kg) from the same cohort were tested over two successive regimes, Fall-Winter (FW) and Winter-Spring (WS) at Lanigan, Saskatchewan, Canada. The steers received forage-based rations in both regimes where the individual feed intake was measured with automatic feeding units. During the trial, the reticulo-rumen (RTMP) and rectal (RCT) temperatures were simultaneously measured every 5 min using telemetric devices. These were used to calculate the circadian parameters (Midline Estimating Statistic Of Rhythms, amplitude, and acrophase/peak time) for both temperature measures. Growth and efficiency performance traits were also determined for all steers. Each steer was assigned into inefficient, neutral, and efficient classes based on the SD of the residual feed intake (RFI), residual gain (RG), and residual intake and gain (RIG) within each year and feeding regime. Higher (p < 0.0003) RTMP and rectal temperature MESORs were observed in the Fall-Winter compared to the Winter-Spring regime. While the two test regimes were different (p < 0.05) for the majority of the RTMP or RCT temperature parameters, they did not differ (p > 0.10) with the production efficiency profiles. The heritability estimates were higher in FW (0.78 ± 0.18 vs. 0.56 ± 0.26) than WS (0.50 ± 0.18 vs. 0.47 ± 0.22) for the rumen and rectal MESORs, respectively. There were positive genetic correlations between the two regimes for the RTMP (0.69 ± 0.21) and RCT (0.32 ± 0.59). There was a negative correlation (p < 0.001) between body temperature and ambient temperature. The high heritability estimates and genetic correlations for rumen and rectal temperature parameters demonstrate their potential as beef genetic improvement tools of economic traits associated with the parameters. However, there are limited practical implications of using only the core-body temperature as a proxy for production efficiency traits for beef steers during winter.
Spatial confinement of sliver nanoparticles in nitrogen-doped carbon framework with high catalytic activity and long-term cycling

The development of efficient, economical and stable oxygen reduction reaction (ORR) electro-catalysts is crucial to energy storage-conversion technology. Reducing metal dimension to nanosize is a promising approach to maximize its efficiency, whereas the migration and aggregation of nanoparticles have severely hampered their large-scale applications. Herein, we report a new catalyst of N-doped carbon-coated Ag nano-particles (Ag NP@N-C), wherein Ag nanoparticles are confined by N-doped carbon framework. This as-synthesized Ag NP@N-C exhibits excellent ORR performance with a half-wave potential of 0.83 V and a limit-current density of 7.03 mA cm−2 in an alkaline medium. More importantly, its durability (cycling for 3600 min), methanol resistance ability in alkaline solutions and catalytic properties in rechargeable zinc-air battery outperform those of commercial Pt/C catalyst and other similar Ag-based catalysts reported so far. The main reason stems from the fact that the interaction between Ag nanoparticles and the support of N-doped carbon can be enhanced by the co-work of pyridine nitrogen and carbon vacancy, rationalizing uniform dispersion of Ag particles. Taking into account its simplicity and high electrochemical properties, we believe that spatial confinement might take an effective trajectory to develop new and large-scale catalysts. Graphical Abstract We prepared a Ag NP@N-C-900 catalyst by a in-situ assisted spatial confinement method. This obtained Ag NP@N-C-900 possesses superior ORR performance with a half-wave potential of 0.83 V, excellent stability and methanol resistance ability. Attractively, the primary zinc–air battery based on the Ag NP@N-C-900 air-cathode offers a long cycle of 3600 minutes as well as excellent durability. The catalytic activity and stability exceed most of the Ag-based catalysts reported so far, and are completely comparable to commercially available Pt/C. Spatial confinement of sliver nanoparticles in nitrogen-doped carbon framework with high catalytic activity and long-term cycling.
Structural brain signatures of frailty, defined as accumulation of self-reported health deficits in older adults

Background Frailty in older adults has been associated with reduced brain health. However, structural brain signatures of frailty remain understudied. Our aims were: (1) Explore associations between a frailty index (FI) and brain structure on magnetic resonance imaging (MRI). (2) Identify the most important FI features driving the associations. Methods We designed a cross-sectional observational study from a population-based study (The Irish Longitudinal Study on Aging: TILDA). Participants aged ≥50 years who underwent the wave 3 MRI sub-study were included. We measured cortex, basal ganglia, and each of the Desikan-Killiany regional volumes. Age-and sex-adjusted correlations were performed with a 32-item self-reported FI that included conditions commonly tested for frailty in research and clinical settings. A graph theory analysis of the network composed by each FI item and cortex volume was performed. White matter fiber integrity was quantified using diffusion tensor imaging (DTI). Results In 523 participants (mean age 69, 49% men), lower cortex and thalamic volumes were independently associated with higher FI. Sensory and functional difficulties, diabetes, polypharmacy, knee pain, and self-reported health were the main FI associations with cortex volume. In the network analysis, cortex volume had a modest influence within the frailty network. Regionally, higher FI was significantly associated with lower volumes in both orbitofrontal and temporal cortices. DTI analyses revealed inverse associations between the FI and the integrity of some association bundles. Conclusion The FI used had a recognizable but subtle structural brain signature in this sample. Only some FI deficits were directly associated with cortex volume, suggesting scope for developing FIs that include metrics more specifically related with brain health in future aging neuroscience studies.
Psymberin, a marine-derived natural product, induces cancer cell growth arrest and protein translation inhibition

Colorectal cancer (CRC) is the third most prevalent form of cancer in the United States and results in over 50,000 deaths per year. Treatments for metastatic CRC are limited, and therefore there is an unmet clinical need for more effective therapies. In our prior work, we coupled high-throughput chemical screens with patient-derived models of cancer to identify new potential therapeutic targets for CRC. However, this pipeline is limited by (1) the use of cell lines that do not appropriately recapitulate the tumor microenvironment, and (2) the use of patient-derived xenografts (PDXs), which are time-consuming and costly for validation of drug efficacy. To overcome these limitations, we have turned to patient-derived organoids. Organoids are increasingly being accepted as a “standard” preclinical model that recapitulates tumor microenvironment cross-talk in a rapid, cost-effective platform. In the present work, we employed a library of natural products, intermediates, and drug-like compounds for which full synthesis has been demonstrated. Using this compound library, we performed a high-throughput screen on multiple low-passage cancer cell lines to identify potential treatments. The top candidate, psymberin, was further validated, with a focus on CRC cell lines and organoids. Mechanistic and genomics analyses pinpointed protein translation inhibition as a mechanism of action of psymberin. These findings suggest the potential of psymberin as a novel therapy for the treatment of CRC.
Association between daily eating frequency and mortality in people with diabetes: Findings from NHANES 1999–2014

Background Previous studies have shown that increasing the frequency of eating is beneficial in terms of cardiovascular metabolic risk factors; however, limited evidence is available for the association between daily eating frequency and mortality, especially in people with diabetes. Therefore, we aimed to explore the association between eating frequency and long-term mortality in populations with diabetes. Methods We selected 4,924 individuals suffering from diabetes (mean age: 57.77 years; 51.3% men) from the National Health and Nutrition Examination Survey (NHANES) between 1999 and 2014. Daily eating frequency was used as the exposure factor in this study. We extracted the mortality data from the National Death Index records and matched them with the population of NHANES. All participants were followed up from the date of getting enrolled in NHANES to 31 December 2015. Multivariate Cox proportional hazards regression, Kaplan–Meier survival curves, and restricted cubic spline were used to assess the associations between eating frequency and all-cause and cause-specific mortality among people with diabetes. Results During 34,950 person–years of follow-up, 1,121 deaths were documented, including 272 cardiovascular disease (CVD)-related deaths and 156 cancer-related deaths. After adjusting for confounding factors, the daily eating frequency was linearly inversely associated with all-cause and CVD-related mortality, and the HR (95% CIs) for per one-time increment of eating frequency was 0.88 (0.80–0.98) and 0.77 (0.63–0.93), respectively. Sensitivity analyses showed that the main results and statistical significance were still stable. Conclusion Higher eating frequency was independently related to lower all-cause and CVD-related mortality in people with diabetes, which can be used as a potential strategy for daily-diet management among populations suffering from diabetes.
Assessing the pathogenicity of BRCA1/2 variants of unknown significance: Relevance and challenges for breast cancer precision medicine

Introduction Breast cancer (BC) is the leading cause of cancer-related death in women worldwide. Pathogenic variants in BRCA1 and BRCA2 genes account for approximately 50% of all hereditary BC, with 60-80% of patients characterized by Triple Negative Breast Cancer (TNBC) at an early stage phenotype. The identification of a pathogenic BRCA1/2 variant has important and expanding roles in risk-reducing surgeries, treatment planning, and familial surveillance. Otherwise, finding unclassified Variants of Unknown Significance (VUS) limits the clinical utility of the molecular test, leading to an “imprecise medicine”. Methods We reported the explanatory example of the BRCA1 c.5057A>C, p.(His1686Pro) VUS identified in a patient with TNBC. We integrated data from family history and clinic-pathological evaluations, genetic analyses, and bioinformatics in silico investigations to evaluate the VUS classification. Results Our evaluation posed evidences for the pathogenicity significance of the investigated VUS: 1) association of the BRCA1 variant to cancer-affected members of the family; 2) absence of another high-risk mutation; 3) multiple indirect evidences derived from gene and protein structural analysis. Discussion In line with the ongoing efforts to uncertain variants classification, we speculated about the relevance of an in-depth assessment of pathogenicity of BRCA1/2 VUS for a personalized management of patients with BC. We underlined that the efficient integration of clinical data with the widest number of supporting molecular evidences should be adopted for the proper management of patients, with the final aim of effectively guide the best prognostic and therapeutic paths.
The effect of concentrated pomegranate juice on biomarkers of inflammation, oxidative stress, and sex hormones in overweight and obese women with polycystic ovary syndrome: A randomized controlled trial

Polycystic ovary syndrome (PCOS) is a common gynecological endocrine disorder. Pomegranate juice (PJ) has been known to play anti‐inflammatory and antioxidant roles. However, the effects of PJ on inflammation, oxidative stress, and sex hormones in PCOS patients are very little studied, and thus more studies are needed. This randomized controlled trial enrolled 44 women diagnosed with PCOS according to the Rotterdam criteria, body mass index (BMI) ≥ 25 kg/m2, and aged 18–40 years old. Participants were randomly assigned to take 45 ml/day of concentrated PJ or a control group without intervention. Some biomarkers of sex hormones, inflammation, and oxidative stress were quantified at baseline and after the 8‐week intervention. Compared with the controls, serum testosterone levels were significantly decreased in overweight and obese women with PCOS who supplemented with concentrated PJ (−0.004 ± 0.013 vs. 0.039 ± 0.013, p = .039). However, we did not observe significant differences in luteinizing hormone (LH) and sex hormone‐binding globulin (SHBG) levels and inflammation and oxidative stress factors between the two groups after adjustment for confounding variables. An 8‐week supplementation with concentrated PJ could effectively improve testosterone levels in overweight and obese women with PCOS. This study was registered at www.irct. ir (IRCT20191109045383N1).
A structured sub-pixel target detection method base on manifold learning method

The manifold learning theory is firstly used to transform the hyperspectral images into a low-dimension feature spaces. The reconstruction error is computed to get discriminative information. Then a structured matched subspace detector is developed. This method can effectively avoid the contamination by targets and spectral anomalies to backgrounds subspace and detect sub-pixel targets with better performance than traditional methods.
Digital imaging software versus the “eyeball” method in quantifying steatosis in a liver biopsy

Steatotic livers represent a potentially underutilized resource to increase the donor graft pool; however, 1 barrier to the increased utilization of such grafts is the heterogeneity in the definition and the measurement of macrovesicular steatosis (MaS). Digital imaging software (DIS) may better standardize definitions to study posttransplant outcomes. Using HALO, a DIS, we analyzed 63 liver biopsies, from 3 transplant centers, transplanted between 2016 and 2018, and compared macrovesicular steatosis percentage (%MaS) as estimated by transplant center, donor hospital, and DIS. We also quantified the relationship between DIS characteristics and posttransplant outcomes using log-linear regression for peak aspartate aminotransferase, peak alanine aminotransferase, and total bilirubin on postoperative day 7, as well as logistic regression for early allograft dysfunction. Transplant centers and donor hospitals overestimated %MaS compared with DIS, with better agreement at lower %MaS and less agreement for higher %MaS. No DIS analyzed liver biopsies were calculated to be >20% %MaS; however, 40% of liver biopsies read by transplant center pathologists were read to be >30%. Percent MaS read by HALO was positively associated with peak aspartate aminotransferase (regression coefficient= 1.041.081.12, p<0.001), peak alanine aminotransferase (regression coefficient =1.041.081.12, p<0.001), and early allograft dysfunction (OR=1.101.401.78, p=0.006). There was no association between HALO %MaS and total bilirubin on postoperative day 7 (regression coefficient =0.991.011.04, p=0.3). DIS provides reproducible quantification of steatosis that could standardize MaS definitions and identify phenotypes associated with good clinical outcomes to increase the utilization of steatite livers.
Incubator-independent perfusion system integrated with microfluidic device for continuous electrophysiology and microscopy readouts

Advances in primary and stem cell derived neuronal cell culture techniques and abundance of available neuronal cell types have enabled in vitro neuroscience as a substantial approach to model in vivo neuronal networks. Survival of the cultured neurons is inevitably dependent on the cell culture incubators to provide stable temperature and humidity and to supply required CO2 levels for controlling the pH of culture medium. Therefore, imaging and electrophysiology recordings outside of the incubator are often limited to the short-term experimental sessions. This restricts our understanding of physiological events to the short snapshots of recorded data while the major part of temporal data is neglected. Multiple custom-made and commercially available platforms like integrated on-stage incubators have been designed to enable long-term microscopy. Nevertheless, long-term high-spatiotemporal electrophysiology recordings from developing neuronal networks needs to be addressed. In the present work an incubator-independent polydimethylsiloxane-based double-wall perfusion chamber was designed and integrated with multi-electrode arrays (MEAs) electrophysiology and compartmentalized microfluidic device to continuously record from engineered neuronal networks at sub-cellular resolution. Cell culture media underwent iterations of conditioning to the ambient CO2 and adjusting its pH to physiological ranges to retain a stable pH for weeks outside of the incubator. Double-wall perfusion chamber and an integrated air bubble trapper reduced media evaporation and osmolality drifts of the conditioned media for two weeks. Aligned microchannel-microfluidic device on MEA electrodes allowed neurite growth on top of the planar electrodes and amplified their extracellular activity. This enabled continuous sub-cellular resolution imaging and electrophysiology recordings from developing networks and their growing neurites. The on-chip versatile and self-contained system provides long-term, continuous and high spatiotemporal access to the network data and offers a robust in vitro platform with many potentials to be applied on advanced cell culture systems including organ-on-chip and organoid models.
Numerical study of grid distribution effect on accuracy of DQ analysis of beams and plates by error estimation of derivative approximation

The accuracy of global methods such as the differential quadrature (DQ) approach is usually sensitive to the grid point distribution. This paper is to numerically study the effect of grid point distribution on the accuracy of DQ solution for beams and plates. It was found that the stretching of grid towards the boundary can improve the accuracy of DQ solution, especially for coarse meshes. The optimal grid point distribution (corresponding to optimal stretching parameter) depends on the order of derivatives in the boundary condition and the number of grid points used. The optimal grid distribution may not be from the roots of orthogonal polynomials. This differs somewhat from the conventional analysis. This paper also proposes a simple and effective formulation for stretching the grid towards the boundary. The error distribution of derivative approximation is also studied, and used to analyze the effect of grid point distribution on accuracy of numerical solutions. Copyright © 2001 John Wiley & Sons, Ltd.
THE MONTE CARLO EVALUATION OF ORTHANT PROBABILITIES FOR MULTIVARIATE NORMAL DISTRIBUTIONS

Summary The calculation of multivariate normal orthant probabilities is practically impossible when the number of variates is greater than five or six, except in very special cases. A transformation of the integral is obtained which enables quite accurate Monte Carlo estimates to be obtained for a fairly high number of dimensions, particularly if control variates are used.
Proline transporters ProT and PutP are required for Staphylococcus aureus infection

Proline acquired via specific transporters can serve as a proteinogenic substrate, carbon and nitrogen source, or osmolyte. Previous reports have documented that Staphylococcus aureus, a major community and nosocomial pathogen, encodes at least four proline transporters, PutP, OpuC, OpuD, and ProP. A combination of genetic approaches and 3H-proline transport assays reveal that a previously unrecognized transporter, ProT, in addition to PutP, are the major proline transporters in S. aureus. Complementation experiments using constitutively expressed non-cognate promoters found that proline transport via OpuD, OpuC, and ProP is minimal. Both proline biosynthesis from arginine and proline transport via ProT are critical for growth when S. aureus is grown under conditions of high salinity. Further, proline transport mediated by ProT or PutP are required for growth in media with and without glucose, indicating both transporters function to acquire proline for proteinogenic purposes in addition to acquisition of proline as a carbon/nitrogen source. Lastly, inactivation of proT and putP resulted in a significant reduction (5 log10) of bacterial burden in murine skin-and-soft tissue infection and bacteremia models, suggesting that proline transport is required to establish a S. aureus infection.