Miracle-dz/UniFAR-FTUs huggingface dataset:
Investigation of the probable homo-dimer model of the Xeroderma pigmentosum complementation group A (XPA) protein to represent the DNA-binding core

Abstract The Xeroderma pigmentosum complementation group A (XPA) protein functions as a primary damage verifier and as a scaffold protein in nucleotide excision repair (NER) in all higher organisms. New evidence of XPA’s existence as a dimer and the redefinition of its DNA-binding domain (DBD) raises new questions regarding the stability and functional position of XPA in NER. Here, we have investigated XPA’s dimeric status with respect to its previously defined DBD (XPA98-219) as well as with its redefined DBD (XPA98-239). We studied the stability of XPA98-210 and XPA98-239 homo-dimer systems using all-atom molecular dynamics simulation, and we have also characterized the protein–protein interactions (PPI) of these two homo-dimeric forms of XPA. After conducting the root mean square deviation (RMSD) analyses, it was observed that the XPA98-239 homo-dimer has better stability than XPA98-210. It was also found that XPA98-239 has a larger number of hydrogen bonds, salt bridges, and hydrophobic interactions than the XPA98-210 homo-dimer. We further found that Lys, Glu, Gln, Asn, and Arg residues shared the major contribution toward the intermolecular interactions in XPA homo-dimers. The binding free energy (BFE) analysis, which used the molecular mechanics Poisson–Boltzmann method (MM-PBSA) and the generalized Born and surface area continuum solvation model (GBSA) for both XPA homo-dimers, also substantiated the positive result in favor of the stability of the XPA98-239 homo-dimer. Communicated by Ramaswamy H. Sarma
The Effects of Dynamic-range Automatic Gain Control on Sentence Intelligibility With a Speech Masker in Simulated Cochlear Implant Listening

Objectives: “Channel-linked” and “multi-band” front-end automatic gain control (AGC) were examined as alternatives to single-band, channel-unlinked AGC in simulated bilateral cochlear implant (CI) processing. In channel-linked AGC, the same gain control signal was applied to the input signals to both of the two CIs (“channels”). In multi-band AGC, gain control acted independently on each of a number of narrow frequency regions per channel. Design: Speech intelligibility performance was measured with a single target (to the left, at -15 or -30°) and a single, symmetrically-opposed masker (to the right) at a signal-to-noise ratio (SNR) of -2 decibels. Binaural sentence intelligibility was measured as a function of whether channel linking was present and of the number of AGC bands. Analysis of variance was performed to assess condition effects on percent correct across the two spatial arrangements, both at a high and a low AGC threshold. Acoustic analysis was conducted to compare postcompressed better-ear SNR, interaural differences, and monaural within-band envelope levels across processing conditions. Results: Analyses of variance indicated significant main effects of both channel linking and number of bands at low threshold, and of channel linking at high threshold. These improvements were accompanied by several acoustic changes. Linked AGC produced a more favorable better-ear SNR and better preserved broadband interaural level difference statistics, but did not reduce dynamic range as much as unlinked AGC. Multi-band AGC sometimes improved better-ear SNR statistics and always improved broadband interaural level difference statistics whenever the AGC channels were unlinked. Multi-band AGC produced output envelope levels that were higher than single-band AGC. Conclusions: These results favor strategies that incorporate channel-linked AGC and multi-band AGC for bilateral CIs. Linked AGC aids speech intelligibility in spatially separated speech, but reduces the degree to which dynamic range is compressed. Combining multi-band and channel-linked AGC offsets the potential impact of diminished dynamic range with linked AGC without sacrificing the intelligibility gains observed with linked AGC.
Load-Velocity Relationship in National Paralympic Powerlifters: A Case Study.

PURPOSE To examine the relationships between different loading intensities and movement velocities in the bench-press exercise (BP) in Paralympic powerlifters. METHODS A total of 17 national Paralympic powerlifters performed maximum dynamic strength tests to determine their BP 1-repetition maximum (1RM) in a Smith-machine device. A linear position transducer was used to measure movement velocity over a comprehensive range of loads. Linear-regression analysis was performed to establish the relationships between the different bar velocities and the distinct percentages of 1RM. RESULTS Overall, the correlations between bar velocities and %1RM were strong over the entire range of loads (R2 .80-.91), but the precision of the predictive equations (expressed as mean differences [%] between actual and predicted 1RM values) were higher at heavier loading intensities (∼20% for loads ≤70% 1RM and ∼5% for loads ≥70% 1RM). In addition, it seems that these very strong athletes (eg, 1RM relative in the BP = 2.22 [0.36] kg·kg-1, for male participants) perform BP 1RM assessments at lower velocities than those previously reported in the literature. CONCLUSIONS The load-velocity relationship was strong and consistent in Paralympic powerlifters, especially at higher loads (≥70% 1RM). Therefore, Paralympic coaches can use the predictive equations and the reference values provided here to determine and monitor the BP loading intensity in national Paralympic powerlifters.
Design Effects of Screen-Captured Tutorials on Student Achievement

This paper reports findings from an experimental study of the effects of using differentiated screen-captured multimedia tutorials to teach technology integration skills to preservice educators. A homogeneous set of participants (N=96) were randomly assigned to one of four treatment groups. Participants in each group completed a web-based instructional module using screen captured tutorials developed as Graphic plus Text, Video, Video plus Narration, and Video plus Text. A post-test was administered following the module completion to assess both conceptual recall and task performance. Participants receiving video plus narration tutorials outperformed those in other groups, particularly those receiving only video. These findings are supported in the literature through the cognitive load principles of modality and redundancy. These results add to the growing body of knowledge about the design and development of multimedia instructional materials and invite furtí)er inquiry into related covariates that potentially influence the design of screen captured tutorials. 310 I Joe Winslow, Ph.D., Jerenny Dickerson, Ed.D. & Cheng-Yuan Lee, Ph.D.
Shot Scale Analysis in Movies by Convolutional Neural Networks

The apparent distance of the camera from the subject of a filmed scene, namely shot scale, is one of the prominent formal features of any filmic product, endowed with both stylistic and narrative functions. In this work we propose to use Convolutional Neural Networks for the automatic classification of shot scale into Close-, Medium-, or Long-shots. The development of such a tool allows for investigating the relationship between shot scale computed of large movie corpora and the viewers' emotional involvement, for purposes such as movie recommendation, stylistic analysis, and film therapy, to name a few. Training and testing are performed on the full filmographies by six different authors (Scorsese, Godard, Tarr, Fellini, Antonioni, and Bergman) for a total number of 120 movies analysed second by second. Classification results are widely superior to state-of-the-art, with an overall accuracy around 94%.
Study of Clinical Characteristics and Cytokine Profiles of Asthmatic Children with Rhinovirus Infection during Acute Asthma Exacerbation at National Hospital of Pediatrics

Background In children with asthma, the viral infection of airways is usually a main cause of acute asthma exacerbation and hospitalization. However, few studies on clinical and biomolecular characteristics of asthmatic children in this field have been done, especially in emergent countries. Objective This study described the clinical and biological characteristics of asthmatic children who had acute asthma exacerbation and rhinovirus (RV) infection. Methods Children under 15 years of age hospitalized for acute asthma exacerbation were included. They underwent clinical examination and peripheral blood analyses for the cytokine profile. The severity of acute asthma exacerbation was evaluated by Pediatric Asthma Score (PAS). Healthy children under 15 years of age were also invited in this study. Results One hundred fifteen asthmatic children were included in this study. There were 18.2% of mild PAS, 37.4% of moderate PAS, and 44.4% of severe PSA. Among them, 63/115 (54.8%) asthmatic children had positive RV infection (RV+). The percentages of asthmatic children with RV+ had increased polymorphonuclear leucocytes were significantly higher than asthmatic children with RV−. There were no significant differences of the concentrations of non-Th2-related cytokines in asthmatic children with RV− and RV+. The concentration of Th2-related cytokines (IL-5 and IL-13) in asthmatic children with RV+ was significantly higher than those with RV−. However, there was no significant difference for the cytokine profile between mild, moderate, and severe asthma. Conclusion RV infection is a main cause of acute asthma exacerbation in children with asthma. The increase of Th2-related cytokines, especially IL-5 and IL-13, is a relevant biomarker for RV infection in asthmatic children with severe exacerbation.
Intraorganismal genetic heterogeneity as a source of genetic variation in modular macroalgae

Genetic diversity is considered a key factor of population survival and evolution, especially in changing environments. Genetic diversity arises from mutations in the DNA sequence of cell lines and from there it reaches the level of organisms, populations, and regions. However, many previous studies have not considered the organism architecture or pattern of thallus construction, ignoring the potential genetic complexities that intraorganismal genetic heterogeneity could generate in modular organisms. In seaweeds, modularity and clonality exist in many species. Modular organization has been related to advantages in terms of rapid construction and recovery after the loss of individual modules, which have their own demographic properties as they generate, mature, senesce, and die. Based on recent evidence from the literature, we suggest that modules also have their own genetic properties. Specifically, modular seaweeds have two possible sources of genetic diversity at the individual level: the heterozygosity of the genotypes composing the genet, and genetic heterogeneity among the modules within a genet (i.e., intraclonal genetic variability). Both sources of genetic diversity can have ecological and evolutionary consequences, and most of them must be considered in research on modular seaweeds. Linking intraorganismal genetic diversity with clonal architecture and propagation styles may help us to understand important ecological and evolutionary processes such as speciation modes, invasive capacities, or farming potential.
The Synergistic Effects of the Glutathione Precursor, NAC and First-Line Antibiotics in the Granulomatous Response Against Mycobacterium tuberculosis

Mycobacterium tuberculosis (M. tb), the causative bacterial agent responsible for tuberculosis (TB) continues to afflict millions of people worldwide. Although the human immune system plays a critical role in containing M. tb infection, elimination proves immensely more challenging. Consequently, there has been a worldwide effort to eradicate, and limit the spread of M. tb through the conventional use of first-line antibiotics. Unfortunately, with the emergence of drug resistant and multi-drug resistant strains of M. tb the archetypical antibiotics no longer provide the same ascendancy as they once did. Furthermore, when administered, these first-line antibiotics commonly present severe complications and side effects. The biological antioxidant glutathione (GSH) however, has been demonstrated to have a profound mycobactericidal effect with no reported adverse consequences. Therefore, we examined if N-Acetyl Cysteine (NAC), the molecular precursor to GSH, when supplemented in combination with suboptimal levels of standalone first-line antibiotics would be sufficient to completely clear M. tb infection within in vitro derived granulomas from healthy subjects and individuals with type 2 diabetes (T2DM). Our results revealed that by virtue of immune modulation, the addition of NAC to subprime levels of isoniazid (INH) and rifampicin (RIF) was indeed capable of inducing complete clearance of M. tb among healthy individuals.
FACTS: A Hierarchical Task-based Control Model of Speech Incorporating Sensory Feedback

We present a computational model of speech motor control that integrates vocal tract state prediction with sensory feedback. This hierarchical model, called FACTS, incorporates both a high-level and low-level controller. The high-level controller orchestrates linguistically-relevant speech tasks, which are represented as desired constrictions along the vocal tract (e.g., closure of the lips). The output of the high-level controller is passed to a low-level controller that can issue motor commands at the level of the speech articulators in order to accomplish the desired constrictions. In order to generate these articulatory motor commands, the low-level articulatory controller relies on an estimate of the current state of the vocal tract. This estimate combines internal predictions about the consequences of issued motor commands with auditory and somatosensory feedback from the vocal tract using an Unscented Kalman Filter based state estimation method. FACTS is able to reproduce several important aspects of human speech behavior such as: (i) stable speech behavior in the presence of noisy motor and sensory systems, (ii) partial acoustic compensation to auditory feed-back perturbations, (iii) complete compensations to mechanical perturbations only when they interfere with current production goals, and (iv) the observed relationship between sensory acuity and response to sensory perturbations.
Response of Cisplatin Resistant Skov-3 Cells to [Pt(O,O′-Acac)(γ-Acac)(DMS)] Treatment Revealed by a Metabolomic 1H-NMR Study

The novel [Pt(O,O′-acac)(γ-acac)(DMS)], Ptac2S, Pt(II) complex has recently gained increasing attention as a potential anticancer agent for its pharmacological activity shown in different tumor cell lines, studied both in vitro and in vivo. The mechanism of action of Ptac2S, operating on non-genomic targets, is known to be very different from that of cis-[PtCl2(NH3)2], cisplatin, targeting nucleic acids. In this work, we evaluated the cytotoxicity of Ptac2S on the cisplatin resistant Epithelial Ovarian Carcinoma (EOC), SKOV-3 cells, by the MTT assay. A 1H-NMR metabolomic approach coupled with multivariate statistical analysis was used for the first time for Ptac2S to figure out the biological mechanisms of action of the complex. The metabolic variations of intracellular metabolites and the composition of the corresponding extracellular culture media were compared to those of cisplatin (cells were treated at the IC50 doses of both drugs). The reported comparative metabolomic analysis revealed a very different metabolic profile between Ptac2S and cisplatin treated samples, thus confirming the different mechanism of action of Ptac2S also in the Epithelial Ovarian Carcinoma (EOC), SKOV-3 cells line. In particular, higher levels of pyruvate were observed in Ptac2S treated, with respect to cisplatin treated, cells (in both aqueous and culture media). In addition, a very different lipid expression resulted after the exposure to the two drugs (Ptac2S and cisplatin). These results suggest a possible explanation for the Ptac2S ability to circumvent cisplatin resistance in SKOV-3 cells.
Postoperative chemoradiotherapy versus radiotherapy alone for elderly cervical cancer patients with positive margins, lymph nodes, or parametrial invasion

Objective Women with cervical cancer (CC) found to have positive surgical margins, positive lymph nodes, and/or parametrial invasion receive a survival benefit from postoperative chemoradiotherapy (CRT) vs. radiation therapy (RT) alone. However, older women may not benefit to the same extent, as they are at increased risk of death from non-oncologic causes as well as toxicities from oncologic treatments. This study sought to evaluate whether there was a survival benefit of CRT over RT in elderly patients with cervical cancer. Methods The National Cancer Database was queried for patients ≥70 years old with newly diagnosed IA2, IB, or IIA CC and positive margins, parametrial invasion, and/or positive nodes on surgical resection. Statistics included logistic regression, Kaplan-Meier overall survival (OS), and Cox proportional hazards modeling analyses. Results Altogether, 166 patients met inclusion criteria; 62 (37%) underwent postoperative RT and 104 (63%) underwent postoperative CRT. Younger patients and those living in areas of higher income were less likely to receive CRT, while parametrial invasion and nodal involvement were associated with an increased likelihood (p<0.05 for all). There were no OS differences by treatment type. Subgroup analysis by number of risk factors, as well as each of the 3 risk factors separately, also did not reveal any OS differences between cohorts. Conclusion In the largest such study to date, older women with postoperative risk factor(s) receiving RT alone experienced similar survival as those undergoing CRT. Although causation is not implied, careful patient selection is paramount to balance treatment-related toxicity risks with theoretical outcome benefits.
New Approaches to the Integration of Navigation Systems for Autonomous Unmanned Vehicles (UAV)

The article presents an overview of the theoretical and experimental work related to unmanned aerial vehicles (UAVs) motion parameters estimation based on the integration of video measurements obtained by the on-board optoelectronic camera and data from the UAV’s own inertial navigation system (INS). The use of various approaches described in the literature which show good characteristics in computer simulations or in fairly simple conditions close to laboratory ones demonstrates the sufficient complexity of the problems associated with adaption of camera parameters to the changing conditions of a real flight. In our experiments, we used computer simulation methods applying them to the real images and processing methods of videos obtained during real flights. For example, it was noted that the use of images that are very different in scale and in the aspect angle from the observed images in flight makes it very difficult to use the methodology of singular points. At the same time, the matching of the observed and reference images using rectilinear segments, such as images of road sections and the walls of the buildings look quite promising. In addition, in our experiments we used the projective transformation matrix computation from frame to frame, which together with the filtering estimates for the coordinate and angular velocities provides additional possibilities for estimating the UAV position. Data on the UAV position determining based on the methods of video navigation obtained during real flights are presented. New approaches to video navigation obtained using the methods of conjugation rectilinear segments, characteristic curvilinear elements and segmentation of textured and colored regions are demonstrated. Also the application of the method of calculating projective transformations from frame-to-frame is shown which gives estimates of the displacements and rotations of the apparatus and thereby serves to the UAV position estimation by filtering. Thus, the aim of the work was to analyze various approaches to UAV navigation using video data as an additional source of information about the position and velocity of the vehicle.
Fully Convolutional Siamese Networks for Change Detection

This paper presents three fully convolutional neural network architectures which perform change detection using a pair of coregistered images. Most notably, we propose two Siamese extensions of fully convolutional networks which use heuristics about the current problem to achieve the best results in our tests on two open change detection datasets, using both RGB and multispectral images. We show that our system is able to learn from scratch using annotated change detection images. Our architectures achieve better performance than previously proposed methods, while being at least 500 times faster than related systems. This work is a step towards efficient processing of data from large scale Earth observation systems such as Copernicus or Landsat.
Instance Enhancing Loss: Deep Identity-Sensitive Feature Embedding for Person Search

Person search, which is vital for intelligent surveillance, aims at detecting and re-identifying pedestrians from whole monitoring images. However, due to the inaccurate pedestrian detections and extremely few instances per training identity, it remains challenging to learn discriminative representations only by labeled identities for person search. To this end, this paper proposes a novel loss function called instance enhancing loss (IEL) to learn deep identity-sensitive features by introducing unlabeled identity information. Specifically, the proposed IEL can selectively annotate unlabeled identities with similar appearances to labeled identities, and utilize these unlabeled identities in conjunction with labeled identities to train the person search network. The amount of unlabeled identities used as labeled instances can be quantitatively adjusted. Moreover, the proposed IEL is trainable and easy to optimize by back propagation algorithms. Extensive experiments on two benchmark datasets, namely CUHK-SYSU and PRW, show that our method outperforms state-of-the-arts for person search.
Pitch Characteristics of L2 English Speech by Chinese Speakers: A Large-scale Study

AI-powered English learning apps are used by hundreds of millions of people across the globe on a daily basis. This presents a great opportunity for the study of L2 speech. On one hand, the amount of data accessible for research is very large and rapidly growing; on the other hand, new theories and understanding of L2 speech can be continually tested and revised through real-life and real-time applications. This paper presents a study of pitch characteristics of L2 English speech using a large-scale dataset from a language learning app. Our dataset contains 180,000 spoken utterances which amount to 240 hours of speech. The results show that compared to L1, L2 English has narrower pitch range and slower rate of pitch change, but more small “ripples” on the pitch contour. The percentage of F 0 rise time is higher in L2, and the maximum F 0 in an utterance is realized later (with respect to the onset of the word on which the maximum F 0 resides). These results suggest that the influence of L1 on L2 prosody is more complex than previously demonstrated, and they shed light on L2 prosody assessment and learning.