Miracle-dz/UniFAR-FTUs huggingface dataset:
Efficacy of Early (≤ 24 Hours), Late (25–72 Hours), and Delayed (>72 Hours) Surgery with Magnetic Resonance Imaging-Confirmed Decompression in American Spinal Injury Association Impairment Scale Grades C and D Acute Traumatic Central Cord Syndrome Caused by Spinal Stenosis

The therapeutic significance of timing of decompression in acute traumatic central cord syndrome (ATCCS) caused by spinal stenosis remains unsettled. We retrospectively examined a homogenous cohort of patients with ATCCS and magnetic resonance imaging (MRI) evidence of post-treatment spinal cord decompression to determine whether timing of decompression played a significant role in American Spinal Injury Association (ASIA) motor score (AMS) 6 months following trauma. We used the t test, analysis of variance, Pearson correlation coefficient, and multiple regression for statistical analysis. During a 19-year period, 101 patients with ATCCS, admission ASIA Impairment Scale (AIS) grades C and D, and an admission AMS of ≤95 were surgically decompressed. Twenty-four of 101 patients had an AIS grade C injury. Eighty-two patients were males, the mean age of patients was 57.9 years, and 69 patients had had a fall. AMS at admission was 68.3 (standard deviation [SD] 23.4); upper extremities (UE) 28.6 (SD 14.7), and lower extremities (LE) 41.0 (SD 12.7). AMS at the latest follow-up was 93.1 (SD 12.8), UE 45.4 (SD 7.6), and LE 47.9 (SD 6.6). Mean number of stenotic segments was 2.8, mean canal compromise was 38.6% (SD 8.7%), and mean intramedullary lesion length (IMLL) was 23 mm (SD 11). Thirty-six of 101 patients had decompression within 24 h, 38 patients had decompression between 25 and 72 h, and 27 patients had decompression >72 h after injury. Demographics, etiology, AMS, AIS grade, morphometry, lesion length, surgical technique, steroid protocol, and follow-up AMS were not statistically different between groups treated at different times. We analyzed the effect size of timing of decompression categorically and in a continuous fashion. There was no significant effect of the timing of decompression on follow-up AMS. Only AMS at admission determined AMS at follow-up (coefficient = 0.31; 95% confidence interval [CI]:0.21; p = 0.001). We conclude that timing of decompression in ATCCS caused by spinal stenosis has little bearing on ultimate AMS at follow-up.
Does contingent biofeedback improve cardiac interoception? A preregistered replication of Meyerholz, Irzinger, Withöft, Gerlach, and Pohl (2019) using the heartbeat discrimination task in a randomised control trial

Meyerholz, Irzinger, Withöft, Gerlach, and Pohl (2019) reported on a comparably large effect (d = 1.21) of a contingent biofeedback procedure on cardiac accuracy as assessed by the heartbeat tracking task. However, this task has recently been criticized as a measure of interoceptive accuracy. We aimed to replicate this finding by using the well-validated heartbeat discrimination task and to compare the biofeedback with a deep breathing and a control condition (viewing a film clip). The trial was preregistered at open science framework (https://osf.io/9fxn6). Overall, 93 participants were randomized to one of the three conditions and the heartbeat discrimination task was presented prior and after the 20-minutes training sessions. The study had a power of . 86 to detect a medium-sized effect in the biofeedback group and a power of . 96 to detect a medium-sized interaction of intervention group and time. A general tendency for improvement in heartbeat detection accuracy was found across intervention groups (d = 0.19, p = .08); however, groups did not differ significantly. In particular, there was no significant interaction of intervention group and time (f = .00, p = .98) and no reliable effect for the biofeedback group (d = 0.15, p = .42). One limitation is that a different, but well-validated task was used to quantify interoceptive accuracy. This study suggests that biofeedback might not improve interoceptive accuracy in the cardiac domain, but effects seem to depend on the specific task applied.
Uncultivated Viral Populations Dominate Estuarine Viromes on the Spatiotemporal Scale

This is the first systematic study about spatial and temporal variation of virioplankton communities in estuaries by using deep metagenomics sequencing. It is among the highest-quality viromic data sets to date, showing remarkably consistent sequencing depth and quality across samples. ABSTRACT Viruses are ubiquitous and abundant in the oceans, and viral metagenomes (viromes) have been investigated extensively via several large-scale ocean sequencing projects. However, there have not been any systematic viromic studies in estuaries. Here, we investigated the viromes of the Delaware Bay and Chesapeake Bay, two Mid-Atlantic estuaries. Deep sequencing generated a total of 48,190 assembled viral sequences (>5 kb) and 26,487 viral populations (9,204 virus clusters and 17,845 singletons), including 319 circular viral contigs between 7.5 kb and 161.8 kb. Unknown viruses represented the vast majority of the dominant populations, while the composition of known viruses, such as pelagiphage and cyanophage, appeared to be relatively consistent across a wide range of salinity gradients and in different seasons. A difference between estuarine and ocean viromes was reflected by the proportions of Myoviridae, Podoviridae, Siphoviridae, Phycodnaviridae, and a few well-studied virus representatives. The difference in viral community between the Delaware Bay and Chesapeake Bay is significantly more pronounced than the difference caused by temperature or salinity, indicating strong local profiles caused by the unique ecology of each estuary. Interestingly, a viral contig similar to phages infecting Acinetobacter baumannii (“Iraqibacter”) was found to be highly abundant in the Delaware Bay but not in the Chesapeake Bay, the source of which is yet to be identified. Highly abundant viruses in both estuaries have close hits to viral sequences derived from the marine single-cell genomes or long-read single-molecule sequencing, suggesting that important viruses are still waiting to be discovered in the estuarine environment. IMPORTANCE This is the first systematic study about spatial and temporal variation of virioplankton communities in estuaries using deep metagenomics sequencing. It is among the highest-quality viromic data sets to date, showing remarkably consistent sequencing depth and quality across samples. Our results indicate that there exists a large pool of abundant and diverse viruses in estuaries that have not yet been cultivated, their genomes only available thanks to single-cell genomics or single-molecule sequencing, demonstrating the importance of these methods for viral discovery. The spatiotemporal pattern of these abundant uncultivated viruses is more variable than that of cultured viruses. Despite strong environmental gradients, season and location had surprisingly little impact on the viral community within an estuary, but we saw a significant distinction between the two estuaries and also between estuarine and open ocean viromes.
The effect of in-hospital physiotherapy on handgrip strength and physical activity levels after cardiac valve surgery: a randomized controlled trial.

BACKGROUND Patients who undergo cardiac valve surgery undertake routine physical therapy program. Despite its routine use, its influence on physical activity level post- surgery has not been illustrated. This study was to investigate whether 5 days of in-hospital physiotherapy could improve physical activity levels after cardiac valve surgery. METHODS The study is a single-blind randomized controlled trial which performed in Cardiothoracic Surgery Department. Patients who underwent cardiac valve surgery (n=34) for confirmed cardiac valve disorders were assessed during hospitalization. The intervention group received a daily post-operative physiotherapy intervention, consisting of individualized mobilization, breathing exercises, ambulation with or without a walking aid. There was no physiotherapy treatment in the control group. Measurements: physical activity was assessed with the handgrip strength test and the timed up and go test. RESULTS The treatment group showed significantly greater handgrip strength [20.58 (7.17) vs. 12.96 (4.65) kg] and less time on the timed up and go test [5.92 (2.91) vs. 6.53 (1.60) s] compared to the control group on the 5th post-operative day. Whilst there was no significant difference on the timed up and go test between the 2 groups, handgrip strength on the 5th post-operative day was significantly different between the 2 groups. CONCLUSIONS Patients who received physiotherapy during hospitalization showed increased levels of handgrip strength and physical activity on the 5th day after cardiac valve surgery compared to the control group. The clinical value of increased levels of physical activity after in-hospital physiotherapy following cardiac valve surgery requires further investigation.
Rapid rotational magneto-acousto-electrical tomography with filtered back-projection algorithm based on plane waves

Magneto-acousto-electrical tomography (MAET) is designed to produce conductivity images with high spatial resolution for a conducting object. In a previous study, for an irregular conductor, transverse scanning and rotational methods with a focus transducer were combined to collect complete electrical information. This kind of method, however, is time-consuming because of the transverse scanning procedure. In this study, we proposed a novel imaging method based on plane ultrasound waves and a new aspect of projection in rotational MAET. In the proposed method, we achieved the projection in each rotation angle by using plane waves rather than mechanical scanning of the focus waves along the transverse direction. Thus, the imaging time was significantly saved. To verify the proposed method, we derived a measurement formula containing a lateral integration, which built the relationship between the measurement formula and the projection under each rotation angle. Next, we constructed two different numerical models to compute magneto-acousto-electrical signals by using a finite element method and reconstructed the corresponding conductivity parameter images based on a filtered back-projection algorithm. Then, simulated signals under different signal-to-ratios (6, 20, 40, and 60 dB) were generated to test the performance of the proposed algorithm. To improve the image quality, we further analysed the influence of the filters and the frequency scaling factors embedded in the filtered back-projection algorithm. Moreover, we computed the L2 norm of the error in case of different frequency scaling factors and measurement noises. Finally, we conducted a phantom experiment with a 64-element linear phased array transducer (center frequency of 2.7 MHz) and reconstructed the conductivity parameter images of the circular phantom with an elliptical hole. The experimental results demonstrated the feasibility and time-efficiency of the proposed rapid rotational MAET.
All-Atom Folding Simulations of the Villin Headpiece from Stochastically Selected Coarse-Grained Structures

We discuss the application of a novel efficient protocol for the numerical simulation of the folding dynamics of single domain proteins from the only knowledge of primary sequence. Our approach is based on the combination of a Monte Carlo (MC) coarse-grained evolution followed by all-atom molecular dynamics (MD) simulations in explicit solvent. The coarse-grained model simplifies the protein's energy landscape and allows it to evolve rapidly toward viable starting conformations for MD. A general fine-graining algorithm is then used to reconstruct the full atomic detail of the protein. All atom MD simulations in explicit water are then employed to investigate the protein's conformational evolution toward the native state. We discuss the application of this novel approach to the Villin headpiece, a widely studied test system for folding studies, for which we obtain and maintain an RMS deviation from the NMR structure of 2.4 A for the core region and 3.7 A for the whole protein. Finally, the analysis of the .
Levitational Cell Cytometry for Forensics

Here, a method for label-free, real-time interrogation, monitoring, detection and sorting of biological rare cells in magnetically-suspended heterogeneous samples is developed. To achieve this, heterogeneous populations of cells were levitated and confined in a microcapillary channel. This strategy enables spatiotemporal differential magnetic levitation of rare fragile dead cells equilibrating at different heights based on the balance between magnetic and corrected gravitational forces. In addition, sorting of fragile rare dead cell populations is monitored in real-time. This technique provides a broadly applicable label-free tool for high resolution, real-time research, as well as forensic evidence processing of rape kits. This method is validated with forensic mock samples dating back to 2003, isolating sperm from epithelial fraction with >90% efficiency and >97% purity. Overall, this method reduces the processing time by over 20-fold down to 20 minutes, eliminating centrifugation and labels, and providing an inexpensive and a high-yield alternative to the current centrifuge-based differential extraction techniques. It can potentially facilitate the forensic downstream genomic analyses, accelerating the identification of suspects, and advancing public safety.
Concurrent vs sequential chemoradiotherapy for patients with advanced non–small-cell lung cancer

Supplemental Digital Content is available in the text Abstract Background: Chemotherapy in combination with thoracic radiotherapy yields significant results in patients with advanced non–small-cell lung cancer (NSCLC) compared with thoracic radiotherapy alone. However, whether concurrent or sequential delivery of chemotherapy combined with thoracic radiotherapy is optimal remains unclear. Herein, we conducted a systematic review and meta-analysis of randomized controlled trials (RCTs) to evaluate the efficacy and safety of concurrent vs sequential chemoradiotherapy in patients with NSCLC. Methods: PubMed, EmBase, and Cochrane Library were systematically searched for RCTs focusing on concurrent and sequential chemoradiotherapy for patients with NSCLC. The pooled-effect estimate was calculated using the random-effects model. Sensitivity, subgroup, and publication biases were also evaluated. A total of 14 RCTs (2634 patients with NSCLC) were selected for the final meta-analysis. Results: Compared with sequential chemoradiotherapy, concurrent chemoradiotherapy did not increase the 1-year survival rates; however, concurrent chemoradiotherapy significantly increased the 2-, 3-, 4-, and 5-year survival rates. Moreover, although there were no significant differences between concurrent and sequential chemoradiotherapy in terms of distant relapse and locoregional plus distant relapse, concurrent chemoradiotherapy significantly reduced the risk of locoregional relapse. Furthermore, concurrent chemoradiotherapy yielded positive results with respect to overall response rates. Unfortunately, concurrent chemoradiotherapy could result in esophagitis, nausea/vomiting, and reduced leukocyte and platelet counts in patients with NSCLC. Conclusion: Compared with sequential chemoradiotherapy, concurrent chemoradiotherapy may be significantly beneficial in terms of long-term survival and locoregional relapse, although it increases the risk of grade 3 (or greater) adverse events.
Oxidative Dissolution of Metals in Organic Solvents

Dissolution of metals in organic solvents is relevant to various application fields, such as metal extraction from ores or secondary resources, surface etching or polishing of metals, direct synthesis of organometallic compounds, and separation of metals from other compounds. Organic solvents for dissolution of metals can offer a solution when aqueous systems fail, such as separation of metals from metal oxides, because both the metal and metal oxide could codissolve in aqueous acidic solutions. This review critically discusses organic media (conventional molecular organic solvents, ionic liquids, deep-eutectic solvents and supercritical carbon dioxide) for oxidative dissolution of metals in different application areas. The reaction mechanisms of dissolution processes are discussed for various lixiviant systems which generally consist of oxidizing agents, chelating agents, and solvents. Different oxidizing agents for dissolution of metals are reviewed such as halogens, halogenated organics, donor–acceptor electron-transfer systems, polyhalide ionic liquids, and others. Both chemical and electrochemical processes are included. The review can guide researchers to develop more efficient, economic, and environmentally friendly processes for dissolution of metals in their elemental state.
Differences between cancer patients and others who use medicinal Cannabis

Background Cancer patients have been at the forefront of policy discussions leading to legalization of medical Cannabis (marijuana). Unfortunately, Cannabis use among those with cancer is poorly understood. Methods A diverse group of patients seeking certification for medical Cannabis in the state of Michigan were surveyed at the time of their presentation to medical dispensaries. The survey assessed demographics, employment/disability, pain, physical functioning, mental health, mode of Cannabis use, and frequency/amount of Cannabis use. Chi-square and t-tests were performed to compare those who did and did not endorse cancer diagnosis. Results Analysis of data from 1485 adults pursuing medical Cannabis certification, including 72 (4.8%) reporting a cancer diagnosis, indicated that those with cancer were older [mean age 53.4 years (SD = 10.5) vs. 44.7 years (SD = 13.0); p<0.001] than those without cancer. They also differed regarding employment status (p<0.001; working: 20.8% vs. 46.2%; disabled: 44.4% vs. 26.5% for those with vs. those without cancer, respectively). Those with cancer used less Cannabis (p = 0.033 for quantity used) and used Cannabis less often (p = 0.032 for frequency of use); they less frequently endorsed smoking Cannabis (80% vs 91%; p = 0.015). There was a non-significant trend to increased edible use in those with cancer (57% vs. 44%; p = 0.052). Conclusions Patients with cancer who are seeking medical Cannabis are different from those seeking medical Cannabis without cancer, and they report using Cannabis differently. Further research to characterize the patterns and consequences of Cannabis use in cancer patients is needed.
Plasma Nucleosomes Are Associated With Mortality in Pediatric Acute Respiratory Distress Syndrome

Supplemental Digital Content is available in the text. OBJECTIVES: Circulating nucleosomes and their component histones have been implicated as pathogenic in sepsis and acute respiratory distress syndrome in adults. However, their role in pediatric acute respiratory distress syndrome is unknown. DESIGN: We performed a prospective cohort study in children with acute respiratory distress syndrome, with plasma collection within 24 hours of acute respiratory distress syndrome onset. We associated nucleosome levels with severity of acute respiratory distress syndrome and with nonpulmonary organ failures and tested for association of nucleosomes with PICU mortality and ventilator-free days at 28 days in univariate and multivariable analyses. We also performed proteomics of DNA-bound plasma proteins in a matched case-control study of septic children with and without acute respiratory distress syndrome in order to identify specific histone proteins elevated in acute respiratory distress syndrome. SETTING: Large academic tertiary-care PICU. PATIENTS: Intubated children meeting Berlin criteria for acute respiratory distress syndrome. INTERVENTIONS: None. MEASUREMENTS AND MAIN RESULTS: We enrolled 333 children with acute respiratory distress syndrome, with 69 nonsurvivors (21%). Plasma nucleosomes were correlated with acute respiratory distress syndrome severity and with the number of nonpulmonary organ failures at acute respiratory distress syndrome onset. Nucleosomes were higher (p < 0.001) in nonsurvivors (0.40 [interquartile range, 0.20–0.71] arbitrary units) relative to survivors (0.10 [interquartile range, 0.04–0.25] arbitrary units). Nucleosomes were associated with PICU mortality in multivariable analysis (adjusted odds ratio 1.84 per 1 sd increase; 95% CI, 1.38–2.45; p < 0.001). Nucleosomes were also associated with a lower probability of being extubated alive by day 28 after multivariable adjustment (adjusted subdistribution hazard ratio, 0.74; 95% CI, 0.63–0.88; p = 0.001). Proteomic analysis demonstrated higher levels of the core nucleosome histones H2A, H2B, H3, and H4 in septic children with acute respiratory distress syndrome, relative to septic children without acute respiratory distress syndrome. CONCLUSIONS: Plasma nucleosomes are associated with acute respiratory distress syndrome severity, nonpulmonary organ failures, and worse outcomes in pediatric acute respiratory distress syndrome.
Comment on the Optimal Parameters to Derive Intrinsically Disordered Protein Conformational Ensembles from Small-Angle X-ray Scattering Data Using the Ensemble Optimization Method.

The Ensemble Optimization Method (EOM) is a popular approach to describe small-angle X-ray scattering (SAXS) data from highly disordered proteins. The EOM algorithm selects subensembles of coexisting states from large pools of randomized conformations to fit the SAXS data. Based on the unphysical bimodal radius of gyration (Rg) distribution of conformations resulting from the EOM analysis, a recent article (Fagerberg et al. J. Chem. Theory Comput. 2019, 15 (12), 6968-6983) concluded that this approach inadequately described the SAXS data measured for human Histatin 5 (Hst5), a peptide with antifungal properties. Using extensive experimental and synthetic data, we explored the origin of this observation. We found that the one-bead-per-residue coarse-grained representation with averaged scattering form factors (provided in the EOM as an add-on to represent disordered missing loops or domains) may not be appropriate for EOM analyses of scattering data from short (below 50 residues) proteins/peptides. The method of choice for these proteins is to employ atomistic models (e.g., from molecular dynamics simulations) to sample the protein conformational landscape. As a convenient alternative, we have also improved the coarse-grained approach by introducing amino acid specific form factors in the calculations. We also found that, for small proteins, the search for relatively large subensembles of 20-50 conformers (as implemented in the original EOM version) more adequately describes the conformational space sampled in solution than the procedures optimizing the ensemble size. Our observations have been added as recommendations into the information for EOM users to promote the proper utilization of the program for ensemble-based modeling of SAXS data for all types of disordered systems.