Miracle-dz/UniFAR-FTUs huggingface dataset:
Profile conditional random fields for modeling protein families with structural information

A statistical model of protein families, called profile conditional random fields (CRFs), is proposed. This model may be regarded as an integration of the profile hidden Markov model (HMM) and the Finkelstein-Reva (FR) theory of protein folding. While the model structure of the profile CRF is almost identical to the profile HMM, it can incorporate arbitrary correlations in the sequences to be aligned to the model. In addition, like in the FR theory, the profile CRF can incorporate long-range pair-wise interactions between model states via mean-field-like approximations. We give the detailed formulation of the model, self-consistent approximations for treating long-range interactions, and algorithms for computing partition functions and marginal probabilities. We also outline the methods for the global optimization of model parameters as well as a Bayesian framework for parameter learning and selection of optimal alignments.
A Phase 2, Randomized, Dose-Response Trial of Taprenepag Isopropyl (PF-04217329) Versus Latanoprost 0.005% in Open-Angle Glaucoma and Ocular Hypertension

Purpose: To evaluate the safety of escalating doses of taprenepag isopropyl (PF-04217329), a selective EP2 receptor agonist administered as a topical ophthalmic solution, versus its vehicle (Stage I), and dose-response of taprenepag isopropyl alone and in unfixed combination with latanoprost ophthalmic solution 0.005% versus latanoprost alone (Stage II). Subjects and Methods: Randomized, vehicle- and active-controlled, double-masked, two-stage, dose-finding trial in primary open-angle glaucoma (POAG) or ocular hypertension; first taprenepag isopropyl study in patients (NCT00572455). Study eye: 26 mmHg ≤ intraocular pressure (IOP) <36 mmHg at 8 am and 22 mmHg ≤ IOP <36 mmHg at 10 am, 1 pm, 4 pm. Stage I: 3 cohorts (total n = 67) received 1 drop of taprenepag isopropyl unit dose formulation qPM/eye for 14 days: low dose: 0.0025%, 0.005%, vehicle; middle dose: 0.01%, 0.015%, vehicle; high dose: 0.02%, 0.03%, vehicle. Stage II: 7 groups (total n = 250) received 1 drop of taprenepag isopropyl multidose formulation qPM/eye for 28 days: 0.005%, 0.01%, 0.015% monotherapy; each in unfixed combination with latanoprost 0.005%, or latanoprost monotherapy. Main outcomes: mean change in diurnal IOP, baseline to last visit; adverse events. Results: Stage I at Day 14: statistically significantly greater IOP reductions were observed at all taprenepag isopropyl doses versus vehicle. Stage II at Day 28: statistically significantly greater IOP reductions were observed at all doses of the unfixed combination versus latanoprost monotherapy. At least 1 treatment-emergent adverse event reported for 29/67 (43.3%) subjects in Stage I and 158/250 (63.2%) in Stage II. Conclusions: Taprenepag isopropyl significantly reduces IOP in POAG and ocular hypertension. Taprenepag isopropyl monotherapy is comparable to latanoprost 0.005% in reducing IOP. As demonstrated in this report, the activity of taprenepag isopropyl is additive to that of latanoprost 0.005%. Further studies are required to determine whether it shows similar additivity when administered with other ocular antihypertensive medications.
VDR‐Alien: a novel, DNA‐selective vitamin D3 receptor‐corepressor partnership

The vitamin D receptor (VDR) is a transcription factor that transmits incoming 1,25‐dihy‐droxyvitamin D3 (1α,25(OH)2D3) signaling via combined contact with coactivator proteins and specific DNA binding sites (VDREs), which ultimately results in activation of transcription. In contrast, the mechanisms of transcriptional repression via the VDR are less well understood. This study documents VDR‐dependent transcriptional repression largely via histone deacety‐lase (HDAC) activity. Direct, ligand‐sensitive protein‐protein interaction of the VDR with the nuclear receptor corepressor (NCoR) and a novel corepressor, called Alien, was demonstrated to be comparable but independent of the VDR AF‐2 trans‐activation domain. Functional assays indicated that Alien, but not NCoR, displays selectivity for different VDRE structures for transferring these repressive effects into gene regulatory activities. Moreover, superrepression via Alien was found to be affected only in part by HDAC inhibitors such as trichostatin A. Finally, for a dissociation of VDR‐Alien complexes in vitro and in vivo, higher ligand concentrations were needed than for a dissociation of VDR‐NCoR complexes. This suggests that Alien and NCoR are using different interfaces for interaction with the VDR and different pathways for mediating superrepression, which in turn characterizes Alien as a representative of a new class of corepressors. Taken together, association of the VDR with corepressor proteins provides a further level of transcriptional regulation, which is emerging as a complex network of protein‐protein interaction‐mediated control. —Polly, P., Herdick, M. , Moehren, U. , Baniahmad, A. , Heinzel, T. , Carlberg, C. VDR‐Alien: a novel, VDR‐Alien: a novel, DNA‐selective vitamin D3 receptor‐corepressor partnership. FASEBJ. 14, 1455–1463 (2000)
The Structure of Echovirus Type 12 Bound to a Two-domain Fragment of Its Cellular Attachment Protein Decay-accelerating Factor (CD 55)*

Echovirus type 12 (EV12), an Enterovirus of the Picornaviridae family, uses the complement regulator decay-accelerating factor (DAF, CD55) as a cellular receptor. We have calculated a three-dimensional reconstruction of EV12 bound to a fragment of DAF consisting of short consensus repeat domains 3 and 4 from cryo-negative stain electron microscopy data (EMD code 1057). This shows that, as for an earlier reconstruction of the related echovirus type 7 bound to DAF, attachment is not within the viral canyon but occurs close to the 2-fold symmetry axes. Despite this general similarity our reconstruction reveals a receptor interaction that is quite different from that observed for EV7. Fitting of the crystallographic co-ordinates for DAF34 and EV11 into the reconstruction shows a close agreement between the crystal structure of the receptor fragment and the density for the virus-bound receptor, allowing unambiguous positioning of the receptor with respect to the virion (PDB code 1UPN). Our finding that the mode of virus-receptor interaction in EV12 is distinct from that seen for EV7 raises interesting questions regarding the evolution and biological significance of the DAF binding phenotype in these viruses.
A Study about Principle Component Analysis and Eigenface for Facial Extraction

Facial recognition is one of the most successful applications of image analysis and understanding. This paper presents a Principal Component Analysis (PCA) and eigenface method for facial feature extraction. Several performance metrics, i.e. accuracy, precision, and recall are taken into account as a baseline of experiment. Furthermore, two public data sets, namely SOF (Speech on faces) and MIT CBCL Facerec are incorporated in the experiment. Based on our experimental result, it can be revealed that PCA has performed well in terms of accuracy, precision, and recall metrics by 0.598, 0.63, and 0.598, respectively.
A genetic algorithm for designing optimal patch configurations in GIS

Optimal patch design is a generic problem in which the objective is to find the best configuration of patches subject to multiple criteria. It is a hard problem in spatial geometry relevant to numerous applications in spatial planning and analysis. GIS packages do not have optimal patch design functions and there has been very little research in this area. This paper describes a computer system for solving optimal patch design problems in raster GIS. The method uses a genetic algorithm search heuristic combined with a region-growing programme that generates alternative patch configurations. The version described here solves multiple patch problems and was developed from an earlier version for designing single patches. In tests on a hypothetical planning problem the multi-patch version was found to be more efficient, but less effective, than the single patch version. The last part of the paper discusses outstanding issues regarding the applicability usability and external validity of the system and suggests ideas for further research.
Spatial Logistic Regression for Support-Vector Classification of Hyperspectral Imagery

The traditional use of support-vector machines for hyperspectral imagery exploits spectral information alone; however, classifiers that incorporate spatial context have witnessed increasing interest due to their potential for significant improvement over spectral-only approaches. A new paradigm for spatial-spectral support-vector classification is introduced in which spatial context is included into the logistic regression commonly used with support-vector classifiers to provide a probabilistic output. In experimental results, the proposed approach is compared to methods representative of two prominent families of spatial-spectral support-vector classifiers—composite kernels and postprocessing regularization—and it is observed that the proposed approach provides superior classification accuracy.
Evaluation of Phytochemical Content and Antioxidant Potential of Ocimum gratissimum and Telfairia occidentalis Leaves

Aim: The aim of this study is to compare the phytochemical content and antioxidant potential of Ocimum gratissimum and Telfairia occidentalis leaves. Study Design: This study was made to fit a one-way Analysis of Variance. Place and Duration of Study: This research was carried out in the Department of Premedical Science, Educational Advancement Centre, Ibadan and Pharmaceutical Laboratory of the University of Ibadan, Nigeria between January and June, 2018. Methods: Both plants were purchased from Bodija market in Ibadan, Nigeria. The leaves were removed from the stem and washed with running water to remove contaminants. It was oven dried at 37˚C and milled into powder and extracted with ethanol. The qualitative and quantitative analyses of the phytochemical content as well as antioxidant potential were investigated. Results: The result showed that O. gratissimum is significantly higher in flavonoids content but lower in alkaloids when compared with those of T. occidentalis at P<0.05. No significant difference was observed in the concentrations of saponin, tannin, total phenolics and phytic acid in O. gratissimum when compared with those of T. occidentalis respectively at P<0.05. Antioxidant investigation showed that O. gratissimum is higher in ferric-ion reducing power but lower in ascorbic acid when compared with T. occidentalis respectively at P<0.05. The percentage inhibition of 2,2-diphenyl-1-picryl-hydrazyl-hydrate radical scavenging potential was observed to decrease with decreasing concentration for both plants but that of O. gratissimum was lower when compared with that of T. occidentalis respectively. Conclusion: This pharmacological study is a useful tool for further drug development from the natural plant products.
Four‐weekly infliximab in the treatment of severe hidradenitis suppurativa

DEAR EDITOR, Hidradenitis suppurativa (HS) is a chronic debilitating disorder characterized by the development of comedones, inflammatory nodules, cysts and sinus tracts at apocrine gland-bearing sites. Severe disease may lead to local complications of sinus tract formation, fistula formation and lymphoedema. Constitutional upset and extracutaneous features, including arthritis and interstitial keratitis, may be seen. Quality of life may be severely impaired. Treatment options for severe disease are limited. The beneficial effect of infliximab has been demonstrated at a dosing regimen licensed for use in moderate-to-severe psoriasis, i.e. 5 mg kg 1 repeated 2 and 6 weeks after the initial infusion, then every 8 weeks. This is not the only dosing schedule licensed in the use of infliximab; maintenance doses of ≤7 5 mg kg 1 and intervals of ≥4 weeks are used in inflammatory bowel disease and inflammatory joint disease, respectively, with optional extra doses prescribed for disease flares. The optimal dosing schedule for the use of infliximab, which has a half-life of 9 5 days, in HS has not been determined. Kimball et al. recently demonstrated the superiority of weekly adalimumab [another tumour necrosis factor (TNF)-a antagonist] dosing in HS over the conventional fortnightly dosing schedule in a randomized controlled trial. At our centre, three patients with HS who were treated with infliximab 5 mg kg 1 at weeks 0, 2 and 6, and 8weekly thereafter, were noted to develop ‘wearing off’ of infliximab effect with a disease flare approximately 4 weeks after each infusion. This occurred at 9 months, 11 months and 14 months after commencing the drug. The frequency of infusions was therefore increased to 4-weekly resulting in improved disease control. On this basis, eight subsequent patients with HS were given infliximab infusions at a dose of 5 mg kg 1 at weeks 0 and 2, and 4-weekly thereafter. All patients had undergone pretreatment investigations as recommended by the British Association of Dermatologists’ guidelines for the use of biologic interventions for psoriasis prior to commencing treatment. Hurley stage, Dermatology Life Quality Index (DLQI) and the patient visual analogue score (VAS) for pain were recorded. All patients had disease of such severity that accurate calculation of the Sartorius score was not possible. Patients were monitored every 3 months. To date, 11 patients with disabling Hurley stage 3 disease have been maintained on 4-weekly infliximab infusions at a dose of 5 mg kg 1 at our centre. Baseline patient characteristics are shown in Table 1. Median duration of therapy to date is 49 1 months (Table 2). Median patient follow-up is Table 1 Baseline patient characteristics (n = 11)
Biomechanical Properties of Human Dilated Ascending Aorta

Abstract Aneurysms of ascending aorta are dilatation of the first part of the human aorta. They commonly show no clinical symptoms. This condition increases the risk of aorta dissection, which is a life-threatening condition. In this study we attempted to elucidate the changes in the biomechanical properties that occur in the dilated human ascending aorta. Fourteen specimens of ascending aorta wall were mechanically tested under a uniaxial tensile test. Two specimens from each ascending aorta anterior region were cut in longitudinal and circumferential directions. The samples were stretched until rupture of the sample occurred. The obtained experimental data were processed to determine maximal stress, maximal strain and the tangential modulus of elasticity in the linear part of the stress-strain curve. The obtained results showed a remarkable anisotropy of the ascending aorta tissue. We found higher strength of the tissue in the circumferential direction than in the longitudinal direction. There were no statistically significant differences between the strains of the samples. Tangential modulus of elasticity of the aortic samples in the longitudinal direction was significantly lower than the elastic modulus of the samples in the circumferential direction. The tissue in the circumferential direction is stronger and stiffer than in the longitudinal direction.
Ig gene-like molecule CD31 plays a nonredundant role in the regulation of T-cell immunity and tolerance

CD31 is an Ig-like molecule expressed by leukocytes and endothelial cells with an established role in the regulation of leukocyte trafficking. Despite genetic deletion of CD31 being associated with exacerbation of T cell-mediated autoimmunity, the contribution of this molecule to T-cell responses is largely unknown. Here we report that tumor and allograft rejection are significantly enhanced in CD31-deficient mice, which are also resistant to tolerance induction. We propose that these effects are dependent on an as yet unrecognized role for CD31-mediated homophilic interactions between T cells and antigen-presenting cells (APCs) during priming. We show that loss of CD31 interactions leads to enhanced primary clonal expansion, increased killing capacity, and diminished regulatory functions by T cells. Immunomodulation by CD31 signals correlates with a partial inhibition of proximal T-cell receptor (TCR) signaling, specifically Zap-70 phosphorylation. However, CD31-deficient mice do not develop autoimmunity due to increased T-cell death following activation, and we show that CD31 triggering induces Erk-mediated prosurvival activity in T cells either in conjunction with TCR signaling or autonomously. We conclude that CD31 functions as a nonredundant comodulator of T-cell responses, which specializes in sizing the ensuing immune response by setting the threshold for T-cell activation and tolerance, while preventing memory T-cell death.
Plasmid structural instability associated with pC194 replication functions

The hybrid plasmid pJS37 is composed of the streptococcal plasmid pLS1, which confers tetracycline resistance, and the staphylococcal plasmid pC194, which confers chloramphenicol resistance. When gram-positive bacteria containing pJS37 were grown in the presence of chloramphenicol, four different deleted derivatives accumulated. The deletions in the plasmid enhanced resistance to chloramphenicol by placing the cat gene of pC194 near promoters of pLS1. All four deletions shared a common endpoint that corresponded to the putative target site for DNA strand nicking by the pC194 replication protein, RepH. At the other, variable endpoint, the DNA sequence was similar to the putative RepH target sequence. Alteration of the RepH protein, by in vitro modification of the gene encoding it, eliminated this class of deletions. By extending a previously proposed model for the generation of a different but related class of deletions (B. Michel and S.D. Ehrlich, EMBO J. 5:3691-3696, 1986), a comprehensive model that could generate both classes of deletions is suggested. It proposes that a nicking-closing activity of the plasmid replication protein at its normal target site and, aberrantly, at sites with similar sequence can generate deletions either proximal or distal to the aberrant site during rolling-circle replication of the plasmid.
Resource constrained mapping of data flow graphs onto coarse-grained reconfigurable array

This paper proposes a heuristic algorithm to the resource constrained mapping problem in coarse-grained reconfigurable computing, such that the partition number and communications are co-optimized to improve the application performance. Our approach modifies the network flow algorithm with a customized mapping procedure embedded to satisfy the micro-architecture resource constraints. Additionally, we use integer linear programming to set optimal baseline to the problem. Our algorithms reformulate the cost function by identifying some flaws in previous literatures. The experiment results qualify the benefit gained by our proposed approach.
Chaotic Dynamics and Application of LCR Oscillators Sharing Common Nonlinearity

This paper addresses the problem of sharing common nonlinearity among nonautonomous and autonomous oscillators. By choosing a suitable common nonlinear element with the driving point characteristics capable of bringing out chaotic motion in a combined system, we obtain identical chaotic states. The dynamics of the coupled system is explored through numerical and experimental studies. Employing the concept of common nonlinearity, a simple chaotic communication system is modeled and its performance is verified through Multisim simulation.
Abnormal Hippocampal BDNF and miR-16 Expression Is Associated with Depression-Like Behaviors Induced by Stress during Early Life

Some environmental stressors lead to the onset of depression via inhibiting hippocampal BDNF expression, but other environmental stressors-induced depression exhibits no change in BDNF expression. The underlying mechanisms behind the divergence remain unknown. In this study, depression-like behaviors were induced in rats by maternal deprivation (MD) and chronic unpredictable stress (CUPS). Depression-like behaviors were tested by open field test, forced swimming test, and sucrose consumption test. BDNF and miR-16 expressions in the hippocampus were examined by real-time PCR. MD and CUPS rats crawled less distance, exhibited decreased vertical activity, and produced more fecal pellets than control rats in the open field test. However, MD rats crawled less distance and produced significantly less fecal pellets than CUPS rats. In the forced swimming and sucrose consumption tests, CUPS and MD rats exhibited longer floating time and consumed less sucrose than control rats, but MD rats exhibited shorter floating time and consumed less sucrose than CUPS rats. MD but not CUPS rats showed lower BDNF mRNA and higher miR-16 expression than control rats. In MD rats, BDNF mRNA expression negatively correlated with the expression of miR-16. BDNF expression positively correlated with the total distance rats crawled and vertical activity in the open field test while miR-16 expression negatively correlated the two behaviors. BDNF positively correlated with sucrose preference rate while miR-16 negatively correlated with sucrose preference rate of the sucrose consumption test. Our study suggests that MD and CUPS induced different depression-like behaviors in rats. Depression induced by MD but not CUPS was significantly associated with upregulation of miR-16 and possibly subsequent downregulation of BDNF in hippocampus.
Effects of a 4-Week Neuromuscular Training Program on Movement Competency During the Back-Squat Assessment in Pre– and Post–Peak Height Velocity Male Athletes

Abstract Dobbs, IJ, Oliver, JL, Wong, MA, Moore, IS, Myer, GD, and Lloyd, RS. Effects of a 4-week neuromuscular training program on movement competency during the back-squat assessment in pre– and post–peak height velocity male athletes. J Strength Cond Res 35(10): 2698–2705, 2021—The back-squat assessment (BSA) is a novel movement screen to detect functional deficits; however, its sensitivity to detect meaningful changes in movement competency after exposure to short-term neuromuscular training remains unclear. Twenty-six pre– and 22 post–peak height velocity (PHV) males were divided into experimental (EXP) and control groups (CON) and performed the BSA before and after a twice weekly, 4-week neuromuscular training intervention. Intra-rater reliability was determined by rating both EXP group's baseline BSA on 3 separate sessions. Intraclass correlation coefficient (ICC) revealed very strong agreement for BSA total score in pre-PHV (ICC ≥ 0.81) and post-PHV (ICC ≥ 0.97) groups across all sessions, but systematic bias was evident in the pre-PHV group for sessions 1–2. Analysis of kappa values for BSA individual criteria showed greater variability for pre-PHV (K ≥ 0.31) than post-PHV (K ≥ 0.62) across sessions. At baseline, there were no differences in total score between the EXP and CON cohorts (p > 0.05). There were significant within-group improvements in total score for the EXP pre-PHV (5.0 to 3.0, effect size [ES] = 0.68) and post-PHV (2.0 to 1.0, ES = 0.82) cohorts, with no changes in total score for either CON groups (p > 0.05). Hip position was the criterion with the greatest improvement for both the EXP pre-PHV (12.0 to 7.0) and post-PHV (7.0 to 0.0) groups. The BSA seems to be a reliable screening tool for measuring movement competency in youth male athletes and was sensitive to adaptations in movement competency after neuromuscular training.