Miracle-dz/UniFAR-FTUs huggingface dataset:
Clinical, Functional, and Physical Activity Outcomes 5 Years Following the Treatment Algorithm of the Delaware-Oslo ACL Cohort Study

Background: Anterior cruciate ligament (ACL) injuries can be treated with or without ACL reconstruction (ACLR), and more high-quality studies evaluating outcomes after the different treatment courses are needed. The purpose of the present study was to describe and compare 5-year clinical, functional, and physical activity outcomes for patients who followed our decision-making and treatment algorithm and chose (1) early ACLR with preoperative and postoperative rehabilitation, (2) delayed ACLR with preoperative and postoperative rehabilitation, or (3) progressive rehabilitation alone. Early ACLR was defined as that performed ≤6 months after the preoperative rehabilitation program, and late ACLR was defined as that performed >6 months after the preoperative rehabilitation program. Methods: We included 276 patients from a prospective cohort study. The patients had been active in jumping, pivoting, and cutting sports before the injury and sustained a unilateral ACL injury without substantial concomitant knee injuries. The patients chose their treatment through a shared decision-making process. At 5 years, we assessed the International Knee Documentation Committee Subjective Knee Form (IKDC-SKF), Knee injury and Osteoarthritis Outcome Score (KOOS), Marx Activity Rating Scale, sports participation, quadriceps muscle strength, single-legged hop performance, and new ipsilateral and contralateral knee injuries. Results: The 5-year follow-up rate was 80%. At 5 years, 64% of the patients had undergone early ACLR, 11% had undergone delayed ACLR, and 25% had had progressive rehabilitation alone. Understandably, the choices that participants made differed by age, concomitant injuries, symptoms, and predominantly level-I versus level-II preinjury activity level. There were no significant differences in any clinical, functional, or physical activity outcomes among the treatment groups. Across treatment groups, 95% to 100% of patients were still active in some kind of sports and 65% to 88% had IKDC-SKF and KOOS scores above the threshold for a patient acceptable symptom state. Conclusions: Patients with ACL injury who were active in jumping, pivoting, and cutting sports prior to injury; who had no substantial concomitant knee injuries; and who followed our decision-making and treatment algorithm had good 5-year knee function and high sport participation rates. Three of 4 patients had undergone ACLR within 5 years. There were no significant differences in any outcomes among patients treated with early ACLR, delayed ACLR, or progressive rehabilitation alone. Level of Evidence: Therapeutic Level II. See Instructions for Authors for a complete description of levels of evidence.
Oligomodal metamaterials with multifunctional mechanics

Significance Mechanical metamaterials are man-made materials with extraordinary properties that come from their geometrical structure rather than their chemical composition. For instance, they can be engineered to be extremely light and stiff; to shrink sideways when compressed, instead of expanding; or to exhibit programmable shape changes. Such properties often rely on zero-energy modes. In this work, we created a class of mechanical metamaterials with zero-energy modes that can exhibit multiple properties at the same time within a single structure. In particular, we created a metamaterial that can either shrink or expand on the side when compressed, depending on how fast it is compressed. These metamaterials could lead to novel adaptable devices for, for example, robotics and energy absorption applications. Mechanical metamaterials are artificial composites that exhibit a wide range of advanced functionalities such as negative Poisson’s ratio, shape shifting, topological protection, multistability, extreme strength-to-density ratio, and enhanced energy dissipation. In particular, flexible metamaterials often harness zero-energy deformation modes. To date, such flexible metamaterials have a single property, for example, a single shape change, or are pluripotent, that is, they can have many different responses, but typically require complex actuation protocols. Here, we introduce a class of oligomodal metamaterials that encode a few distinct properties that can be selectively controlled under uniaxial compression. To demonstrate this concept, we introduce a combinatorial design space containing various families of metamaterials. These families include monomodal (i.e., with a single zero-energy deformation mode); oligomodal (i.e., with a constant number of zero-energy deformation modes); and plurimodal (i.e., with many zero-energy deformation modes), whose number increases with system size. We then confirm the multifunctional nature of oligomodal metamaterials using both boundary textures and viscoelasticity. In particular, we realize a metamaterial that has a negative (positive) Poisson’s ratio for low (high) compression rate over a finite range of strains. The ability of our oligomodal metamaterials to host multiple mechanical responses within a single structure paves the way toward multifunctional materials and devices.
Application of ultrasonic dual-mode artificially intelligent architecture in assisting radiologists with different diagnostic levels on breast masses classification.

PURPOSE We aimed to compare the diagnostic performance and interobserver variability in breast tumor classification with or without the aid of an innovative dual-mode artificial intelligence (AI) architecture, which can automatically integrate information from ultrasonography (US) and shear-wave elastography (SWE). METHODS Diagnostic performance assessment was performed with a test subset, containing 599 images (from September 2018 to February 2019) from 91 patients including 64 benign and 27 malignant breast tumors. Six radiologists (three inexperienced, three experienced) were assigned to read images independently (independent diagnosis) and then make a secondary diagnosis with the knowledge of AI results. Sensitivity, specificity, accuracy, receiver-operator characteristics (ROC) curve analysis and Cohen's κ statistics were calculated. RESULTS In the inexperienced radiologists' group, the average area under the ROC curve (AUC) for diagnostic performance increased from 0.722 to 0.765 (p = 0.050) with secondary diagnosis using US-mode and from 0.794 to 0.834 (p = 0.019) with secondary diagnosis using dual-mode compared with independent diagnosis. In the experienced radiologists' group, the average AUC for diagnostic performance was significantly higher with AI system using the US-mode (0.812 vs. 0.833, p = 0.039), but not for dual-mode (0.858 vs. 0.866, p = 0.458). Using the US-mode, interobserver agreement among all radiologists improved from fair to moderate (p = 0.003). Using the dual-mode, substantial agreement was seen among the experienced radiologists (0.65 to 0.74, p = 0.017) and all radiologists (0.62 to 0.73, p = 0.001). CONCLUSION AI assistance provides a more pronounced improvement in diagnostic performance for the inexperienced radiologists; meanwhile, the experienced radiologists benefit more from AI in reducing interobserver variability.
Re-Applying the Basic Psychological Needs in Exercise Scale to Various Portuguese Exercise Groups: An Analysis of Bifactor Models and Contextual Invariance

This research explored the nature of basic psychological needs in physical activity settings by applying relatively advanced methodological procedures for psychometric assessment. We first re-examined the Basic Psychological Needs in Exercise Scale (BPNES) by reviewing its applicability for physical activity domains among Portuguese respondents. We demonstrated the use of Bifactor Confirmatory Factor Analysis (CFA) and Exploratory Structural Equation Modeling (ESEM) and discussed the practical implications of these models. Next, we tested contextual measurement invariance in order to examine needs universality. Our participants were gym exercisers (n = 1935), physical education students (n = 1449), and athletes (n = 1631), all of whom completed the adapted and validated version of the scale in their respective practice physical activity domains. All models under analysis displayed acceptable to excellent fit; the bifactor ESEM model displayed the best fit. We conducted ancillary bifactor measures to assess scale dimensionality and found that the BPNES is best interpreted as a multidimensional instrument. Through testing for multigroup analysis, the bifactor ESEM did not show contextual invariance. In conclusion, the BPNES should be predominantly used as a multidimensional instrument when assessing basic needs in separate physical activity domains. Basic psychological needs are perceived differently between seemingly similar physical activity contexts. Researchers should measure basic needs as a global factor and use context validated sub-scales.
Incidence of Renal Tract Abnormalities on Ultrasonography in Patients with Spinal Cord Injury: A Retrospective Pilot Study of a Military Cohort Undergoing Long-Term Institutional Rehabilitation

Study Design Retrospective pilot study. Purpose To assess the incidence of renal tract abnormalities using ultrasonography (US) in a military cohort with traumatic spinal cord injury (TSCI) at a tertiary level spinal cord injury center. Overview of Literature Neurogenic bladder in TSCI patients results in significant urological morbidity. There is lack of data for these patients during the first 18 months of long-term rehabilitation in an institutional setting. Methods We retrospectively reviewed patient records to collect data on demographic characteristics, injury level, injury severity, time since injury, bladder management methods (such as an indwelling catheter [IC], clean intermittent catheterization [CIC], or self-voiding [S]); we correlated these data with the findings of the renal tract US. Results The study included 73 out of 81 male participants. The mean patient age was 29.99 years; the study group included 34.2% tetraplegics and 65.8% people with paraplegia. The time since injury was 6–12 months for 42.5% of the subjects and 12–18 months for 57.5% of the subjects. A normal US scan was recorded in 65.7% patients, and bladder trabeculation was the commonest finding in 15.1% of the subjects, followed by hydronephrosis (HDN) in 12.3%, and renal calculus and atrophy in 1.3% participants each. We found 22.22% of the IC group participants had higher US abnormalities than those in the reflex voiding group (statistically non-significant difference, p=0.7). Trabeculations (21.4%) and HDN (19%) were more common in those who had sustained the injury 12–18 months previously as compared to that in those who had injured themselves 6–12 months previously (p=0.04). The proportion of patients who had a normal US scan was higher in the group who sustained the injury 6–12 months previously versus those who had sustained the injury 12–18 months previously; the difference was statistically significant (p=0.02). There was no significant (p=0.72) correlation in the bladder management method, injury level, and renal tract abnormalities between the groups. Conclusions This retrospective study shows that 65% of TSCI participants had no renal tract abnormality on US scan and bladder trabeculation ruled out as the most common finding. Long-term supervised rehabilitation may help achieve good renal quality of life; however, further prospective trials are required on this subject.
Sediment toxicity data and excess simultaneously extracted metals from field‐collected samples: Comparison to United States Environmental Protection Agency benchmarks

US Environmental Protection Agency (USEPA) Procedures for the Derivation of Equilibrium Partitioning Sediment Benchmarks (ESBs) for the Protection of Benthic Organisms: Metal Mixtures are based on the principle that metals toxicity to benthic organisms is determined by bioavailable metals concentrations in porewater. One ESB is based on the difference between simultaneously extracted metal (SEM) and acid volatile sulfide (AVS) concentrations in sediment (excess SEM). The excess SEM ESBs include a lower uncertainty bound, below which most samples (95%) are expected to be “nontoxic” (defined as a bioassay mortality rate ≤24%), and an upper uncertainty bound, above which most samples (95%) are expected to be “toxic” (defined as a mortality rate >24%). Samples that fall between the upper and lower bounds are classified as “uncertain. ” Excess SEM ESBs can, in principle, be improved by normalizing for organic carbon (OC). OC is a binding phase that reduces metals bioavailability. OC normalization should improve the accuracy of bioavailable metal concentration estimates, thus tightening uncertainty bounds. We evaluated field‐collected sediments from 13 studies with excess SEM, OC, and bioassay data (n = 740). Use of the OC‐normalized excess SEM benchmarks did not improve prediction accuracy. The ESB model predicts OC‐normalized excess SEM exceeding the upper benchmark even when toxicity is not observed, because error in the OC normalization model increases at low OC concentrations. To minimize the likelihood of incorrectly identifying nontoxic samples as toxic, we recommend that OC normalization of excess SEM should not be considered for sediments with an OC concentration <1% and is questionable for sediments with an OC concentration of 1%–4%. Additional focused studies are needed to confirm or refine the minimum sediment OC concentrations that are applicable for reducing uncertainty in toxicity predictions due to excess SEM. Integr Environ Assess Manag 2022;18:174–186. © 2021 SETAC
Effect of heat treatment and γ-irradiation on pasting, rheological, and fungal load of whole and dehulled millets

Millets are important food crops in food systems and application of physical treatments could improve the functional properties of millet-based products. Therefore, we investigated the effect of heat and γ-irradiation treatments on the pasting, rheological, and microbial load of whole and dehulled millets (sorghum, foxtail millet, and pearl millet). Moreover, similarity in treatment effect was evaluated by principal component analysis (PCA). The results revealed the significant (p < 0.05) decrease in pasting properties of whole and dehulled millets, except for pasting temperature (71.03 to 74.88 °C). Likewise, significantly (p < 0.05) decreased tendency was observed for all rheological properties, except for phase angle (0.05 to 0.30°) and yield point (13 to 5089). Samples showed a significant (p < 0.05) reduction in fungal growth (89.75 × 104 to 4.46 × 104 CFU/g) compared to control (110.30 × 104 CFU/g). Moreover, samples individually formed 3 clusters (clusters 1: sorghum, 2: pearl millet, and 3: foxtail millet) based on pasting properties, which was confirmed by PCA. Therefore, the findings concluded that the effect of heat and γ-irradiation would be necessary to decrease pasting, rheological, and no microbial growth characteristics of dehulled and whole millets for the development of specific millet-based food products.
Prediction of drug-induced kidney injury in drug discovery

Abstract Drug induced kidney injury is one of the leading causes of failure of drug development programs in the clinic. Early prediction of renal toxicity potential of drugs is crucial to the success of drug candidates in the clinic. The dynamic nature of the functioning of the kidney and the presence of drug uptake proteins introduce additional challenges in the prediction of renal injury caused by drugs. Renal injury due to drugs can be caused by a wide variety of mechanisms and can be broadly classified as toxic or obstructive. Several biomarkers are available for in vitro and in vivo detection of renal injury. In vitro static and dynamic (microfluidic) cellular models and preclinical models can provide valuable information regarding the toxicity potential of drugs. Differences in pharmacology and subsequent disconnect in biomarker response, differences in the expression of transporter and enzyme proteins between in vitro to in vivo systems and between preclinical species and humans are some of the limitations of current experimental models. The progress in microfluidic (kidney-on-chip) platforms in combination with the ability of 3-dimensional cell culture can help in addressing some of these issues in the future. Finally, newer in silico and computational techniques like physiologically based pharmacokinetic modeling and machine learning have demonstrated potential in assisting prediction of drug induced kidney injury.
Global abundance estimates for 9,700 bird species

Significance For the fields of ecology, evolutionary biology, and conservation, abundance estimates of organisms are essential. Quantifying abundance, however, is difficult and time consuming. Using a data integration approach integrating expert-derived abundance estimates and global citizen science data, we estimate the global population of 9,700 bird species (∼92% of all extant bird species). We conclude that there are many rare species, highlighting the need to continue to refine global population estimates for all taxa and the role that global citizen science data can play in this effort. Quantifying the abundance of species is essential to ecology, evolution, and conservation. The distribution of species abundances is fundamental to numerous longstanding questions in ecology, yet the empirical pattern at the global scale remains unresolved, with a few species’ abundance well known but most poorly characterized. In large part because of heterogeneous data, few methods exist that can scale up to all species across the globe. Here, we integrate data from a suite of well-studied species with a global dataset of bird occurrences throughout the world—for 9,700 species (∼92% of all extant species)—and use missing data theory to estimate species-specific abundances with associated uncertainty. We find strong evidence that the distribution of species abundances is log left skewed: there are many rare species and comparatively few common species. By aggregating the species-level estimates, we find that there are ∼50 billion individual birds in the world at present. The global-scale abundance estimates that we provide will allow for a line of inquiry into the structure of abundance across biogeographic realms and feeding guilds as well as the consequences of life history (e.g., body size, range size) on population dynamics. Importantly, our method is repeatable and scalable: as data quantity and quality increase, our accuracy in tracking temporal changes in global biodiversity will increase. Moreover, we provide the methodological blueprint for quantifying species-specific abundance, along with uncertainty, for any organism in the world.
Potential prognostic biomarkers related to immunity in clear cell renal cell carcinoma using bioinformatic strategy

ABSTRACT The clear cell renal cell carcinoma (ccRCC) is the main pathological subtype of renal cell carcinoma. Immune system evasion, one hallmark of cancer, contributes to cancer cells in escaping from the attack of immune cells. In order to identify potential prognostic biomarkers in ccRCC patients and immune cells fraction, we collected and downloaded profiles from The Cancer Genome Atlas (TCGA) database and Gene Expression Omnibus (GEO) database. We obtained 2 modules significantly associated with tumor stage and immune cells; functional enrichment analysis showed that genes in the module ‘yellow’ were significantly enriched in proteins targeting to membrane and ribosome, as well as the oxidative phosphorylation pathway, while genes in the module ‘green’ mainly participate in molecular functions associated with immunity like activation of T cells. Four LncRNAs (LINC00472, AL590094.1, AL365203.3, and AC147651.3) and RPL27A and RPL22L1 in the module ‘yellow’ and two lncRNAs (LINC00426 and AC129507.2) and five protein-coding genes (CSF1, NOD2, ITGAE, CD7, and PDCD1) in the module ‘green’ represented independent prognostic values in patients with ccRCC. Expression of LINC0042, NOD2, CD7, and PDCD1 were significantly correlated with ratio of immune cells (like T cells CD8 and resting mast cells). LINC00426, with significant correlation with immune cell fraction, shows potential prognostic value in ccRCC patients. Our findings provide a strategy in exploring biomarkers with prognostic significance and significant association with the fraction of immune cells. GA
A novel Ca2+ indicator for long-term tracking of intracellular calcium flux.

The major drawback of using Fluo-4 AM is that it requires an organic anion transporter inhibitor, such as probenecid, to prevent leakage. This can hinder the studies that require extended monitoring time and longer cellular retention. To address the issue, a novel Ca2+ indicator, Calbryte 520 AM, was developed. We compared the performance of Fluo-4 AM and Calbryte 520 AM following prolonged incubation periods after cell loading. Cells loaded with Calbryte 520 AM retained the dye for up to 24 h while exhibiting significant fluorescence brightness and superior Fmax/F0 ratios (Fmax: fluorescence intensity upon stimulation; F0: intensity before stimulation). It demonstrated that the longer retention of Calbryte 520 AM can be exploited to accommodate for the extended time required when monitoring calcium dynamics.
Predictors of Arthrofibrosis After Pediatric Anterior Cruciate Ligament Reconstruction: What Is the Impact of Quadriceps Autograft?

Background: Recent literature on arthrofibrosis after anterior cruciate ligament reconstruction (ACLR) in children and adolescents is limited, especially with regards to quadriceps tendon (QT) autograft. The purpose of this study was to identify predictors of arthrofibrosis after ACLR, with attention to the impact of graft type. Methods: Patients that underwent primary ACLR at a tertiary children’s hospital were reviewed for this retrospective case-control study. Those with multiligament reconstructions, lateral extra-articular tenodesis procedures, allografts, or a modified MacIntosh reconstruction were excluded. Arthrofibrosis was defined as a deficit of 10 degrees of extension and/or 20 degrees of flexion at 3 months after ACLR. Univariate analysis was followed by purposeful entry logistic regression to adjust for confounding factors. Results: A total of 378 patients (mean age 15.9±1.7 y, 49.7% female) were included in the analysis, of which there were 180 patellar tendon (PT), 103 hamstrings tendon (HT), and 95 QT grafts. The rate of arthrofibrosis was 1.9% for HT, 6.3% for QT, and 10.0% for PT (P=0.04). Females developed arthrofibrosis more frequently than males (10.6% vs. 3.2%, P=0.004). Those that ultimately experienced this complication had lower median flexion at 6 weeks after ACLR (88 vs. 110 degrees, P<0.001). In multivariate analysis, PT graft raised the odds of arthrofibrosis 6.2 times compared to HT [95% confidence interval (CI): 1.4-27.6, P=0.02], but there were no significant differences between QT and other grafts. Females were at 4.2 times higher odds than males (95% CI: 1.6-10.8; P=0.003). Patients that were unable to attain 90 degrees of flexion 6 weeks after ACLR had 14.7 times higher odds of eventually developing arthrofibrosis (95% CI: 5.4-39.8; P<0.001). Finally, those with an extension deficit of ≥5 degrees 6 weeks after ACLR had 4.7 times higher odds of experiencing this complication (95% CI: 1.8-12.2, P=0.001). Conclusion: The rate of arthrofibrosis with QT autograft is 6.3% after pediatric ACLR. PT autograft, female sex, and motion deficits at 6 weeks after ACLR were predictive of arthrofibrosis in children and adolescents. Level of Evidence: Level III—prognostic study.