Miracle-dz/UniFAR-FTUs huggingface dataset:
Effects of Resistance Exercise Order on the Number of Repetitions Performed to Failure and Perceived Exertion in Untrained Young Males

Abstract Exercise order is an essential variable of resistance training (RT) programs which is usually related to repetition performance. The purpose of this study was to investigate the acute effect of different resistance exercise order on the number of repetitions performed to failure and related ratings of perceived exertion (RPE). Thirteen male adolescents (age: 14.46 ± 1.39 years, body height: 165.31 ± 12.75 cm, body mass: 58.73 ± 12.27 kg, estimated body fat: 21.32 ± 2.84%), without previous experience in RT, performed four resistance exercises: incline leg press (ILP), dumbbell lunge (DL), bench press (BP) and lying barbell triceps extension (TE) in two sequences - Sequence A (SEQA): ILP, DL, BP and TE; sequence B (SEQB): ILP, BP, DL and TE. The exercise sequences were performed in a randomized crossover design with a rest interval of 72h between sessions. Within-subjects analysis showed significant differences in the number of repetitions performed to failure in both sequences, but not in the RPE. Post-hoc tests revealed significant decrements in the number of repetitions from the first to the remaining exercises in both sequences. However, pairwise comparisons did not indicate significant differences between the same exercises performed in different sequences. In conclusion, the results of the current study in adolescents suggest that the main exercises should be performed at the beginning of the RT session.
Transcriptome Analysis of Core Dinoflagellates Reveals a Universal Bias towards “GC” Rich Codons

Although dinoflagellates are a potential source of pharmaceuticals and natural products, the mechanisms for regulating and producing these compounds are largely unknown because of extensive post-transcriptional control of gene expression. One well-documented mechanism for controlling gene expression during translation is codon bias, whereby specific codons slow or even terminate protein synthesis. Approximately 10,000 annotatable genes from fifteen “core” dinoflagellate transcriptomes along a range of overall guanine and cytosine (GC) content were used for codonW analysis to determine the relative synonymous codon usage (RSCU) and the GC content at each codon position. GC bias in the analyzed dataset and at the third codon position varied from 51% and 54% to 66% and 88%, respectively. Codons poor in GC were observed to be universally absent, but bias was most pronounced for codons ending in uracil followed by adenine (UA). GC bias at the third codon position was able to explain low abundance codons as well as the low effective number of codons. Thus, we propose that a bias towards codons rich in GC bases is a universal feature of core dinoflagellates, possibly relating to their unique chromosome structure, and not likely a major mechanism for controlling gene expression.
Feature Based Framework to Detect Diseases, Tumor, and Bleeding in Wireless Capsule Endoscopy

Studying animal locomotion improves our understanding of motor control and aids in the treatment of motor impairment. Mice are a premier model of human disease and are the model system of choice for much of basic neuroscience. High frame rates (250 Hz) are needed to quantify the kinematics of these running rodents. Manual tracking, especially for multiple markers, becomes time-consuming and impossible. Therefore, an automated method is necessary. We propose a method to track the paws of the animal in the following manner: first, segmenting all the possible paws based on color; second, classifying the segmented objects using a support vector machine (SVM) and neural network (NN); third, classifying the objects using the kinematic features of the running animal, coupled with texture features from earlier frames; and finally, detecting and handling collisions to assure the correctness of labelled paws. The proposed method is validated in sixty 1,000 frame video sequences (4 seconds) captured by four cameras from five mice. The total sensitivity for tracking of the front and hind paw is 99.70% using the SVM classifier and 99.76% using the NN classifier. In addition, we show the feasibility of 3D reconstruction using the four camera system.
Improving glaucoma detection using spatially correspondent clusters of damage and by combining standard automated perimetry and optical coherence tomography.

PURPOSE To improve the detection of glaucoma, techniques for assessing local patterns of damage and for combining structure and function were developed. METHODS Standard automated perimetry (SAP) and frequency-domain optical coherence tomography (fdOCT) data, consisting of macular retinal ganglion cell plus inner plexiform layer (mRGCPL) as well as macular and optic disc retinal nerve fiber layer (mRNFL and dRNFL) thicknesses, were collected from 52 eyes of 52 healthy controls and 156 eyes of 96 glaucoma suspects and patients. In addition to generating simple global metrics, SAP and fdOCT data were searched for contiguous clusters of abnormal points and converted to a continuous metric (pcc). The pcc metric, along with simpler methods, was used to combine the information from the SAP and fdOCT. The performance of different methods was assessed using the area under receiver operator characteristic curves (AROC scores). RESULTS The pcc metric performed better than simple global measures for both the fdOCT and SAP. The best combined structure-function metric (mRGCPL&SAP pcc, AROC = 0.868 ± 0.032) was better (statistically significant) than the best metrics for independent measures of structure and function. When SAP was used as part of the inclusion and exclusion criteria, AROC scores increased for all metrics, including the best combined structure-function metric (AROC = 0.975 ± 0.014). CONCLUSIONS A combined structure-function metric improved the detection of glaucomatous eyes. Overall, the primary sources of value-added for glaucoma detection stem from the continuous cluster search (the pcc), the mRGCPL data, and the combination of structure and function.
Kinematic and dynamic adaptive control of a nonholonomic mobile robot using a RNN

In this paper, an adaptive neurocontrol system with two levels is proposed for the motion control of a nonholonomic mobile robot. In the first level, a recurrent network improves the robustness of a kinematic controller and generates linear and angular velocities, necessary to track a reference trajectory. In the second level, another network converts the desired velocities, provided by the first level, into a torque control. The advantage of the control approach is that, no knowledge about the dynamic model is required, and no synaptic weight changing is needed in presence of robot's parameters variation. This capability is acquired through prior 'meta-learning'. Simulation results are demonstrated to validate the robustness of the proposed approach.
Effects of phytase supplementation, individually and in combination, with glycanase, on the nutritive value of wheat and barley.

Four experiments were conducted to examine the effects of a microbial phytase (Natuphos), individually and in combination with glycanase preparations with predominantly xylanase (Natugrain Blend) and glucanase (Natugrain) activities, on the nutritive value of wheat and barley. In Experiment 1, the addition of xylanase and phytase increased the AME of a low-AME wheat by 9.7 and 5.3%, respectively. The differences, however, were not significant (P > 0.05). The combination of the two enzymes increased (P < 0.05) the AME of wheat by 19.0% from 2,646 to 3,149 kcal/kg dry matter. A similar trend was seen in terms of ileal amino acid digestibility values of the wheat-casein diet. In Experiment 2, the AME of normal wheat was increased (P < 0.05) by 6.3 and 4.5%, respectively, with the addition of xylanase and phytase. The combination of the two enzymes, however, did not further improve (P > 0.05) the AME values. In Experiment 3, performance of broilers fed a wheat-based diet was not influenced by the addition of individual enzymes, but increasing inclusion levels of the xylanase plus phytase combination linearly improved weight gain (r = 0.58; P < 0.01) and feed efficiency (r = 0.71; P < 0.001). In Experiment 4, the AME of barley was not influenced by the addition of glucanase or phytase. The enzyme combination marginally (P < 0.07) improved the AME at lower concentrations, but had no benefit at the highest concentration.
Pavlovian Control of Escape and Avoidance

To survive in complex environments, animals need to have mechanisms to select effective actions quickly, with minimal computational costs. As perhaps the computationally most parsimonious of these systems, Pavlovian control accomplishes this by hardwiring specific stereotyped responses to certain classes of stimuli. It is well documented that appetitive cues initiate a Pavlovian bias toward vigorous approach; however, Pavlovian responses to aversive stimuli are less well understood. Gaining a deeper understanding of aversive Pavlovian responses, such as active avoidance, is important given the critical role these behaviors play in several psychiatric conditions. The goal of the current study was to establish a behavioral and computational framework to examine aversive Pavlovian responses (activation vs. inhibition) depending on the proximity of an aversive state (escape vs. avoidance). We introduce a novel task in which participants are exposed to primary aversive (noise) stimuli and characterized behavior using a novel generative computational model. This model combines reinforcement learning and drift-diffusion models so as to capture effects of invigoration/inhibition in both explicit choice behavior as well as changes in RT. Choice and RT results both suggest that escape is associated with a bias for vigorous action, whereas avoidance is associated with behavioral inhibition. These results lay a foundation for future work seeking insights into typical and atypical aversive Pavlovian responses involved in psychiatric disorders, allowing us to quantify both implicit and explicit indices of vigorous choice behavior in the context of aversion.
Quantitative and descriptive comparison of four acoustic analysis systems: vowel measurements.

PURPOSE This study examines accuracy and comparability of 4 trademarked acoustic analysis software packages (AASPs): Praat, WaveSurfer, TF32, and CSL by using synthesized and natural vowels. Features of AASPs are also described. METHOD Synthesized and natural vowels were analyzed using each of the AASP's default settings to secure 9 acoustic measures: fundamental frequency (F0), formant frequencies (F1-F4), and formant bandwidths (B1-B4). The discrepancy between the software measured values and the input values (synthesized, previously reported, and manual measurements) was used to assess comparability and accuracy. Basic AASP features are described. RESULTS Results indicate that Praat, WaveSurfer, and TF32 generate accurate and comparable F0 and F1-F4 data for synthesized vowels and adult male natural vowels. Results varied by vowel for women and children, with some serious errors. Bandwidth measurements by AASPs were highly inaccurate as compared with manual measurements and published data on formant bandwidths. CONCLUSIONS Values of F0 and F1-F4 are generally consistent and fairly accurate for adult vowels and for some child vowels using the default settings in Praat, WaveSurfer, and TF32. Manipulation of default settings yields improved output values in TF32 and CSL. Caution is recommended especially before accepting F1-F4 results for children and B1-B4 results for all speakers.
Effect of dietary sodium zeolite A and graded levels of calcium on growth, plasma, and tibia characteristics of chicks.

Sodium zeolite A (SZA), a synthetic sodium aluminosilicate having high ion-exchange capacity, has been shown to increase eggshell specific gravity in laying hens and to improve Ca utilization in chickens. A 4 x 2 factorial arrangement of treatments was used to investigate the effect of dietary Ca (.6, .8, 1.0, and 1.2%) and SZA (0 and .75%) on growth, plasma, and tibia characteristics of chicks from 5 to 15 days of age. Increasing dietary Ca linearly increased (P less than .05) Ca and alkaline phosphatase (AP) in plasma and increased tibia shearing force and percentage ash, Ca, and P in tibiae. However, dietary Ca linearly decreased (P less than .05) inorganic P and Mg in plasma and Mg and Mn in tibiae. Sodium zeolite A decreased (P less than .05) plasma P and AP and tibia Mg but increased (P less than .05) tibia Ca, Zn, Al, and Mn concentrations. Tibia ash and shearing force were increased in chicks fed SZA receiving inadequate dietary Ca, but they were decreased in chicks fed SZA and excess Ca (Ca by SZA interaction, P less than .05). Tibia density showed a similar trend, but the effect was not significant (Ca by SZA interaction, P less than .12). The addition of SZA enhanced tibia ash, density, and shearing force when dietary Ca was low; however, when added to diets containing 1.2% Ca, SZA reduced many bone mineralization indices with the exception of tibia Ca.
Learning Hedonic Games

Coalitional stability in hedonic games has usually been considered in the setting where agent preferences are fully known. We consider the setting where agent preferences are unknown; we lay the theoretical foundations for studying the interplay between coalitional stability and (PAC) learning in hedonic games. We introduce the notion of PAC stability — the equivalent of core stability under uncertainty — and examine the PAC stabilizability and learnability of several popular classes of hedonic games.
Uniform and piecewise uniform lattice vector quantization for memoryless Gaussian and Laplacian sources

Lattice vector quantizer design procedures for nonuniform sources are presented. The procedures yield lattice vector quantizers with excellent performance and retaining the structure required for fast quantization. Analytical methods for truncating and scaling lattices to be used in vector quantizations are given, and their utility is demonstrated for independent and identically distributed (i.i.d.) Gaussian and Laplacian sources. An analytical technique for piecewise linear multidimensional compandor designs is evaluated for i.i. d. Gaussian and Laplacian sources by comparing its performance to that of the other vector quantizers. >
Mismatch Repair Deficiency, Microsatellite Instability, and Survival: An Exploratory Analysis of the Medical Research Council Adjuvant Gastric Infusional Chemotherapy (MAGIC) Trial

Importance Mismatch repair (MMR) deficiency (MMRD) and microsatellite instability (MSI) are prognostic for survival in many cancers and for resistance to fluoropyrimidines in early colon cancer. However, the effect of MMRD and MSI in curatively resected gastric cancer treated with perioperative chemotherapy is unknown. Objective To examine the association among MMRD, MSI, and survival in patients with resectable gastroesophageal cancer randomized to surgery alone or perioperative epirubicin, cisplatin, and fluorouracil chemotherapy in the Medical Research Council Adjuvant Gastric Infusional Chemotherapy (MAGIC) trial. Design, Setting, and Participants This secondary post hoc analysis of the MAGIC trial included participants who were treated with surgery alone or perioperative chemotherapy plus surgery for operable gastroesophageal cancer from July 1, 1994, through April 30, 2002. Tumor sections were assessed for expression of the MMR proteins mutL homologue 1, mutS homologue 2, mutS homologue 6, and PMS1 homologue 2. The association among MSI, MMRD, and survival was assessed. Main Outcomes and Measures Interaction between MMRD and MSI status and overall survival (OS). Results Of the 503 study participants, MSI results were available for 303 patients (283 with microsatellite stability or low MSI [median age, 62 years; 219 males (77.4%)] and 20 with high MSI [median age, 66 years; 14 males (70.0%)]). A total of 254 patients had MSI and MMR results available. Patients treated with surgery alone who had high MSI or MMRD had a median OS that was not reached (95% CI, 11.5 months to not reached) compared with a median OS among those who had neither high MSI nor MMRD of 20.5 months (95% CI, 16.7-27.8 months; hazard ratio, 0.42; 95% CI, 0.15-1.15; P = .09). In contrast, patients treated with chemotherapy plus surgery who had either high MSI or MMRD had a median OS of 9.6 months (95% CI, 0.1-22.5 months) compared with a median OS among those who were neither high MSI nor MMRD of 19.5 months (95% CI, 15.4-35.2 months; hazard ratio, 2.18; 95% CI, 1.08-4.42; P = .03). Conclusions and Relevance In the MAGIC trial, MMRD and high MSI were associated with a positive prognostic effect in patients treated with surgery alone and a differentially negative prognostic effect in patients treated with chemotherapy. If independently validated, MSI or MMRD determined by preoperative biopsies could be used to select patients for perioperative chemotherapy.
Deciphering Dimerization Modes of PAS Domains: Computational and Experimental Analyses of the AhR:ARNT Complex Reveal New Insights Into the Mechanisms of AhR Transformation

The Aryl hydrocarbon Receptor (AhR) is a transcription factor that mediates the biochemical response to xenobiotics and the toxic effects of a number of environmental contaminants, including dioxins. Recently, endogenous regulatory roles for the AhR in normal physiology and development have also been reported, thus extending the interest in understanding its molecular mechanisms of activation. Since dimerization with the AhR Nuclear Translocator (ARNT) protein, occurring through the Helix-Loop-Helix (HLH) and PER-ARNT-SIM (PAS) domains, is needed to convert the AhR into its transcriptionally active form, deciphering the AhR:ARNT dimerization mode would provide insights into the mechanisms of AhR transformation. Here we present homology models of the murine AhR:ARNT PAS domain dimer developed using recently available X-ray structures of other bHLH-PAS protein dimers. Due to the different reciprocal orientation and interaction surfaces in the different template dimers, two alternative models were developed for both the PAS-A and PAS-B dimers and they were characterized by combining a number of computational evaluations. Both well-established hot spot prediction methods and new approaches to analyze individual residue and residue-pairwise contributions to the MM-GBSA binding free energies were adopted to predict residues critical for dimer stabilization. On this basis, a mutagenesis strategy for both the murine AhR and ARNT proteins was designed and ligand-dependent DNA binding ability of the AhR:ARNT heterodimer mutants was evaluated. While functional analysis disfavored the HIF2α:ARNT heterodimer-based PAS-B model, most mutants derived from the CLOCK:BMAL1-based AhR:ARNT dimer models of both the PAS-A and the PAS-B dramatically decreased the levels of DNA binding, suggesting this latter model as the most suitable for describing AhR:ARNT dimerization. These novel results open new research directions focused at elucidating basic molecular mechanisms underlying the functional activity of the AhR.
Cerebral Perfusion Changes in Post-Concussion Syndrome: A Prospective Controlled Cohort Study

Abstract The biology of post-concussive symptoms is unclear. Symptoms are often increased during activities, and have been linked to decreased cerebrovascular reactivity and perfusion. The aim of this study was to examine cerebral blood flow (CBF) in children with different clinical recovery patterns following mild traumatic brain injury (mTBI). This was a prospective controlled cohort study of children with mTBI (ages 8 to 18 years) who were symptomatic with post-concussive symptoms at one month post-injury (symptomatic, n = 27) and children who had recovered quickly (asymptomatic, n = 24). Pseudo continuous arterial spin labeling magnetic resonance imaging (MRI) was used to quantify CBF. The mTBI groups were imaged at 40 days post-injury. Global and regional CBF were compared with healthy controls of similar age and sex but without a history of mTBI (n = 21). Seventy-two participants (mean age: 14.1 years) underwent neuroimaging. Significant differences in CBF were found: global CBF was higher in the symptomatic group and lower in the asymptomatic group compared with controls, (F(2,69) 9.734; p < 0.001). Post-injury symptom score could be predicted by pre-injury symptoms and CBF in presence of mTBI (adjusted R2 = 0.424; p < 0.001). Altered patterns of cerebral perfusion are seen following mTBI and are associated with the recovery trajectory. Symptomatic children have higher CBF. Children who “recovered” quickly, have decreased CBF suggesting that clinical recovery precedes the cerebral recovery. Further longitudinal studies are required to determine if these perfusion patterns continue to change over time.
Computation of the Schrödinger Equation in the Semiclassical Regime on an Unbounded Domain

The study of this paper is twofold: On the one hand, we generalize the high-order local absorbing boundary conditions (LABCs) proposed in [J. Zhang et al., Comm. Comput. Phys., 10 (2011), pp. 742--766] to compute the Schrodinger equation in the semiclassical regime on an unbounded domain. We analyze the stability of the equation with LABCs and the convergence of the Crank--Nicolson scheme that discretizes it and we conclude that when the rescaled Planck constant $\varepsilon$ gets small, the accuracy deteriorates and the requirements on time step and mesh size get tough. This leads to the second part of our study. We propose an asymptotic method based on the frozen Gaussian approximation. The absorbing boundary condition is dealt with by a simple strategy that all the effects of the Gaussian functions which contribute to the outgoing waves will be eliminated by stopping the Hamiltonian flow of their centers when they get out of the domain of interest. We present numerical examples in both one and two dime.
Amlexanox Inhibits Cerebral Ischemia-Induced Delayed Astrocytic High-Mobility Group Box 1 Release and Subsequent Brain Damage

High-mobility group box 1 (HMGB1) is increased in the cerebrospinal fluid (CSF) and serum during the early and late phases of brain ischemia and is known to contribute to brain damage. However, detailed characterization underlying cell type-specific HMGB1 release and pathophysiological roles of extracellularly released HMGB1 in ischemic brain remain unclear. Here, we examined cell type-specific HMGB1 release and the therapeutic potential of amlexanox, an inhibitor of nonclassical release, and of an anti-HMGB1 antibody against ischemic brain damage. HMGB1 depletion from neuronal nuclei was observed within 3 hours after transient middle cerebral artery occlusion (tMCAO), whereas the intracerebroventricular (i.c.v.) pretreatment with amlexanox blocked HMGB1 release from neurons, resulting in HMGB1 redistribution in the nuclei and cytoplasm. HMGB1 was selectively released from astrocytes 27 hours after tMCAO and this HMGB1 release was blocked by late treatment with amlexanox (i.c.v.) 24 hours after tMCAO. Proximity extension assay revealed that the HMGB1 level was elevated in the CSF at 3 and 27 hours after tMCAO. This late treatment with amlexanox significantly protected the brain from ischemic damage, but its pretreatment 30 minutes before tMCAO failed to show any protection. The late treatment (i.c.v.) with anti-HMGB1 antibody 24 hours after tMCAO also ameliorated ischemic brain damage 48 hours after tMCAO. Thus, the inhibition of brain damage by late treatment with amlexanox or anti-HMGB1 antibody indicates that late HMGB1 release plays a role in the maintenance of stroke-induced brain damage, and the inhibition of this release would be a novel therapeutic target for protection of ischemic brain damage.