Miracle-dz/UniFAR-FTUs huggingface dataset:
Prediction of the Binding Mode between the Small Peptide Inhibitor EBR28 with Integrase through Molecular Modeling Methods

Human immunodeficiency virus type 1 (HIV-1) integrase (IN), which aids the integration of viral DNA into the host chromosome, is an essential enzyme in the lifecycle of this virus and also an important target for the study of anti-HIV drugs. Recently synthesized 12-mer EBR28 which was identified through the yeast two-hybrid system and could strongly bind to IN is one of the most potential small peptide leading compounds inhibiting IN binding to viral DNA. The binding mode of IN core domain and its peptide inhibitor EBR28 was investigated by using molecular docking and molecular dynamics (MD) simulation and confirmed with a semi-empirical binding free energy calculation method, i.e. MM-GBSA model. The results show that EBR28 binds to the interspace between alpha1 helix and alpha5 helix in the IN core domain mainly through hydrophobic interactions, which impedes the dimerization of the two IN monomers and inhibits IN binding to viral DNA in the end. The correlation between calculated and experimental binding free energies is very good (r = 0.88). All of the above simulation results agree well with experimental data, which provide us with some helpful information for designing anti-HIV small peptide drugs based on the structure of IN.
The Mass Function of Void Galaxies in the Sloan Digital Sky Survey Data Release 2

We estimate the mass function of void galaxies in the second public data release of the Sloan Digital Sky Survey from a sample of 1000 galaxies with local density contrasts of δv < -0.6. The galaxy sample is split into ellipticals and spirals using a color-Sérsic index criterion. We estimate the virial masses of ellipticals using the measured spectral line widths along with the observed size. Projection effects and uncertainties in halo properties make mass estimates of spirals more difficult. We use an inversion of the Tully-Fisher relation to estimate the isothermal rotational velocity and introduce a scaling factor to estimate the halo extent. We then fit the measured mass function against a theoretical Press-Schechter model and find that the distribution of galaxies in voids appears to be nearly unbiased compared to the mass.
The TALE Homeodomain Protein Pbx2 Is Not Essential for Development and Long-Term Survival

ABSTRACT Pbx2 is one of four mammalian genes that encode closely related TALE homeodomain proteins, which serve as DNA binding partners for a subset of Hox transcription factors. The expression and contributions of Pbx2 to mammalian development remain undefined, in contrast to the essential roles recently established for family members Pbx1 and Pbx3. Here we report that Pbx2 is widely expressed during embryonic development, particularly in neural and epithelial tissues during late gestation. Despite wide Pbx2 expression, mice homozygous mutant for Pbx2 are born at the expected Mendelian frequencies and exhibit no detectable abnormalities in development and organogenesis or reduction of long-term survival. The lack of an apparent phenotype in Pbx2− /− mice likely reflects functional redundancy, since the Pbx2 protein is present at considerably lower levels than comparable isoforms of Pbx1 and/or Pbx3 in embryonic tissues. In postnatal bone marrow and thymus, however, Pbx2 is the predominant high-molecular-weight (MW)-isoform Pbx protein detectable by immunoblotting. Nevertheless, the absence of Pbx2 has no measurable effect on steady-state hematopoiesis or immune function in adult mice, suggesting possible compensation by low-MW-isoform Pbx proteins present in these tissues. We conclude that the roles of Pbx2 in murine embryonic development, organogenesis, hematopoiesis, immune responses, and long-term survival are not essential.
Differential response of tumor cells and normal fibroblasts to fractionated combined treatment with topotecan and ionizing radiation

Purpose : The impact of the topoisomerase-I inhibitor topotecan (Hycamtin ®) as a single agent or in combination with ionizing radiation on clonogenic cell survival has been evaluated in three tumor cell lines and in normal fibroblasts. Both agents have been applied in a fractionated scheme in order to assess clinically relevant conditions. Materials and methods : Cell inactivation was investigated in human glioblastoma cell lines U118 and U138, lung carcinoma cell line A549 and normal fibroblasts of the skin (HSF6) and lung (CCD32) using the colony formation assay. Results : The glioblastoma cell lines were highly sensitive to the drug, whereas normal fibroblasts were much less sensitive. A significant antagonistic effect of the drug combined with irradiation was found for normal fibroblasts, while glioblastoma cells showed no evidence of interaction, indicating additivity. A549 cells showed a biphasic response to topotecan alone and in combination with irradiation, suggesting induction of resistence to the drug. Conclusion : Differential effects of combined topotecan/radiation treatment were detected between cells of normal tissue and tumor cells, being antagonistic in fibroblasts of the skin and lung, but not in tumor tissue, especially in glioblastoma cells.
Acanthamoeba griffini. Molecular characterization of a new corneal pathogen.

PURPOSE Acanthamoeba was isolated from the cornea of a soft contact lens wearer who had keratitis. The protozoan was also isolated from the contact lens storage case and the domestic water supply used to clean the case. Using morphologic features, all three isolates were identified tentatively as A. griffini, a species not previously associated with keratitis. Complete small subunit ribosomal RNA gene (18S rDNA) sequence analysis was used to characterize further the three isolates. METHODS 18S rDNA was polymerase chain reaction-amplified from whole cell DNA derived from amoebal lysates. The genes were cloned and sequenced. Complete sequences of approximately 2800 base pairs were obtained from each culture and compared wih those stored in a data base for homologous Acantamoeba sequences. RESULTS The isolates were unequivocally identified as A. griffini both by comparison of the gene sequence available for the type strain of the species and the presence of a unique group I intron located within the small subunit rDNA. Sequences obtained for the three isolates were identical, indicating that they were the same strain. CONCLUSIONS The first direct connection between human disease and A. griffini is reported from a case of Acanthamoeba keratitis. The type strain of this species was isolated from a marine environment, but the disease-causing strain ws isolated from a domestic water supply. The DNA sequences obtained confirmed unequivocally the epidemiologic association between a keratitis-causing strain of Acanthamoeba, the contact lens storage case, and the domestic water supply.
A Sensitive and Stable Surface Plasmon Resonance Sensor Based on Monolayer Protected Silver Film

In this paper, we present a stable silver-based surface plasmon resonance (SPR) sensor using a self-assembled monolayer (SAM) as a protection layer and investigated its efficiency in water and 0.01 M phosphate buffered saline (PBS). By simulation, silver-based SPR sensor has a better performance in field enhancement and penetration depth than that of a gold-based SPR sensor, which are 5 and 1.4 times, respectively. To overcome the instability of the bare silver film and investigate the efficiency of the protected layer, the SAM of 11-mercapto-1-undecanol (MUD) was used as a protection layer. Stability experiment results show that the protected silver film exhibited excellent stability either in pure water or 0.01 M PBS buffer. The sensitivity of the silver-based SPR sensor was calculated to be 127.26 deg/RIU (refractive index unit), measured with different concentrations of NaCl solutions. Further, a very high refractive resolution for the silver-based SPR sensor was found to be 2.207 × 10−7 RIU, which reaches the theoretical limit in the wavelength of 632.8 nm for a SPR sensor reported in the literature. Using a mixed SAM of 16-mercaptohexadecanoic acid (MHDA) and a MUD layer with a ratio of 1:10, this immunosensor for the rabbit immunoglobulin G (IgG) molecule with a limit of detection as low as 22.516 ng/mL was achieved.
Fresh Ankle Osteochondral Allograft Transplantation for Tibiotalar Joint Arthritis

Background: Conventional treatment for tibiotalar joint arthritis relies on arthrodesis or prosthetic arthroplasty. Fresh osteochondral allografting is an alternative procedure to replace diseased articular cartilage. Methods: Eleven patients (average age 43 years; range 18 to 65 years) had fresh osteochondral grafting of the tibiotalar joint. The diagnoses were posttraumatic arthritis in seven ankles, osteoarthritis in two, and an osteochondral defect in two. Precise cuts were made using the Agility® (DePuy, Warsaw IN) ankle arthroplasty jigs. Bipolar replacements were used in nine ankles and unipolar in two. Results were evaluated using outcome scores, physical examinations, and standing ankle radiographs.Results: At a minimum followup of 24 (average 33; range 26 to 45) months, six of the 11 ankles had successful grafting procedures. The average AOFAS score preoperatively improved from 55 to 73 postoperatively (p = 0.01). The patients' pain, gait, and walking surface scores were all significantly improved (p < 0.05). Of the five failures three underwent successful repeat allografting and one was revised to a total ankle arthroplasty, and one has had no further surgery. The ankle range of motion arc was 30 degrees or more in six ankles. Additional surgery included five talofibular joint debridements, three repeat graftings, two hardware removals, and one conversion to a prosthetic ankle replacement. There was one intraoperative fibular fracture and one superficial wound infection. The serum of 10 patients tested positive for cytotoxic HLA antibodies postoperatively. Radiographs revealed moderate and severe joint degeneration in six ankles; however, this did not necessarily correlate with a poor outcome. Poor results tended to occur in ankles with a graft-host size mismatch or graft thickness of less than 7 mm. Conclusion: Fresh osteochondral transplantation for tibiotalar joint arthritis is a promising alternative to arthrodesis and prosthetic replacement. Early results demonstrate successful outcomes and good pain relief in over half the patients in this series.
LTE-unlicensed: the future of spectrum aggregation for cellular networks

The phenomenal growth of mobile data demand has brought about increasing scarcity in available radio spectrum. Meanwhile, mobile customers pay more attention to their own experience, especially in communication reliability and service continuity on the move. To address these issues, LTE-Unlicensed, or LTEU, is considered one of the latest groundbreaking innovations to provide high performance and seamless user experience under a unified radio technology by extending LTE to the readily available unlicensed spectrum. In this article, we offer a comprehensive overview of the LTEU technology from both operator and user perspectives, and examine its impact on the incumbent unlicensed systems. Specifically, we first introduce the implementation regulations, principles, and typical deployment scenarios of LTE-U. Potential benefits for both operators and users are then discussed. We further identify three key challenges in bringing LTE-U into reality together with related research directions. In particular, the most critical issue of LTE-U is coexistence with other unlicensed systems, such as widely deployed WiFi. The LTE/WiFi coexistence mechanisms are elaborated in time, frequency, and power aspects, respectively. Simulation results demonstrate that LTE-U can provide better user experience to LTE users while well protecting the incumbent WiFi users' performance compared to two existing advanced technologies: cellular/WiFi interworking and licensed-only heterogeneous networks (Het-Nets).
Cockayne syndrome group A and B proteins converge on transcription-linked resolution of non-B DNA

Significance In this paper we describe a possible pathogenesis for the accelerated aging disease Cockayne syndrome that entails defective transcription through DNA secondary structures leading to activation of the DNA damage response enzyme poly-ADP-ribose polymerase 1 and downstream mitochondrial derangement. These findings are important because they signify a possible new role of transcription in the resolution of DNA structures that form spontaneously and suggest a possible pathogenesis for this accelerated aging disease. Cockayne syndrome is a neurodegenerative accelerated aging disorder caused by mutations in the CSA or CSB genes. Although the pathogenesis of Cockayne syndrome has remained elusive, recent work implicates mitochondrial dysfunction in the disease progression. Here, we present evidence that loss of CSA or CSB in a neuroblastoma cell line converges on mitochondrial dysfunction caused by defects in ribosomal DNA transcription and activation of the DNA damage sensor poly-ADP ribose polymerase 1 (PARP1). Indeed, inhibition of ribosomal DNA transcription leads to mitochondrial dysfunction in a number of cell lines. Furthermore, machine-learning algorithms predict that diseases with defects in ribosomal DNA (rDNA) transcription have mitochondrial dysfunction, and, accordingly, this is found when factors involved in rDNA transcription are knocked down. Mechanistically, loss of CSA or CSB leads to polymerase stalling at non-B DNA in a neuroblastoma cell line, in particular at G-quadruplex structures, and recombinant CSB can melt G-quadruplex structures. Indeed, stabilization of G-quadruplex structures activates PARP1 and leads to accelerated aging in Caenorhabditis elegans. In conclusion, this work supports a role for impaired ribosomal DNA transcription in Cockayne syndrome and suggests that transcription-coupled resolution of secondary structures may be a mechanism to repress spurious activation of a DNA damage response.
Gene expression of heart and adipocyte fatty acid-binding protein in chickens by FQ-RT-PCR.

This study was to detect the expression of heart fatty acid-binding protein (H-FABP) and adipocyte fatty acid-binding protein (A-FABP) gene mRNA in different tissues of Rugao and Luyuan chickens at 56 d and 120 d by real-time fluorescence quantitative reverse transcription polymerase-chain reaction (FQ-RT-PCR). The primers were designed according to the sequences of H-FABP, A-FABP and GAPDH genes in Gallus gallus, which were used as target genes and internal reference gene, respectively. The levels of H-FABP and A-FABP gene expression were detected by SYBR Green I FQ-RT-PCR. The relative H-FABP and A-FABP gene mRNA expression level was calculated with 2 -ΔCt . Melting curve analysis showed a single peak of three genes. Intramuscular fat (IMF) content in breast muscle and leg muscle of the two chicken breeds at 120 d was higher than at 56 d. IMF content in breast muscle and leg muscle at 56 d and 120 d in Luyuan was significantly higher than in Rugao, however, abdominal fat of Luyuan was significantly lower than that of Rugao. The relative H-FABP gene mRNA expression level in cardiac muscle was the highest in both chicken breeds. The relative H-FABP and A-FABP gene expression of different tissues in Luyuan was higher than in Rugao. H-FABP gene mRNA expression had a negative effect on IMF of leg and breast muscles, and was significantly negatively correlated with IMF content. The relative A-FABP gene mRNA level in abdominal fat was higher than in liver. The A-FABP gene mRNA was not expressed in leg, breast and cardiac muscles. A-FABP gene mRNA expression level was significantly positively correlated with abdominal fat and had a significant effect on abdominal fat but not IMF content.
Effect of N-acetyl cysteine and vitamin C on kidney allograft function biomarkers interleukin-18 and neutrophil gelatinase-associated lipocalin.

INTRODUCTION Delayed graft function (DGF) is a consequence of ischemia-reperfusion injuries in kidney allografts, for which no definite treatment is available. The neutrophil gelatinase-associated lipocalin (NGAL) and interleukin-18 (IL-18) are introduced as the most promising urine biomarkers to detect DGF. N-acetylcysteine (NAC) and vitamin C, well-known potent antioxidants that scavenge free radicals, may alleviate kidney injury. This study investigated the protective effects of NAC alone and in combination with vitamin C on DGF, by measuring IL-18 and NGAL in living donor kidney transplantations. MATERIALS AND METHODS Patients transplanted between January 2011 and February 2013 were randomly divided into 3 groups to receive routine anti-rejection medication only (n = 32), NAC plus routine immunosuppressive regimen (NAC group; n = 33), and NAC and vitamin C plus routine regimen (NAC and vitamin C group; n = 19). Urine samples were taken 4 hours and 24 hours after transplantation. Enzyme-linked immunosorbent assay kits were utilized for measuring urine NGAL and IL-18. RESULTS There were no significant differences in the DGF prevalence and its duration between the study arms. Although the levels of NGAL and IL-18 decreased in the NAC and NAC and vitamin C groups, these reductions were not significant. Glomerular filtration rate at 30 and 60 days after transplantation were not significantly different between study groups, either. CONCLUSIONS Our results showed that NAC is a safe drug without significant adverse effects in kidney transplant recipients; however, its potential useful effects on urinary biomarkers of DGF were not illustrated in the present study.
3D inversion of airborne electromagnetic data using a moving footprint

It is often argued that 3D inversion of entire airborne electromagnetic (AEM) surveys is impractical, and that 1D methods provide the only viable option for quantitative interpretation. However, real geological formations are 3D by nature and 3D inversion is required to produce accurate images of the subsurface. To that end, we show that it is practical to invert entire AEM surveys to 3D conductivity models with hundreds of thousands if not millions of elements. The key to solving a 3D AEM inversion problem is the application of a moving footprint approach. We have exploited the fact that the area of the footprint of an AEM system is significantly smaller than the area of an AEM survey, and developed a robust 3D inversion method that uses a moving footprint. Our implementation is based on the 3D integral equation method for computing data and sensitivities, and uses the re-weighted regularised conjugate gradient method for minimising the objective functional. We demonstrate our methodology with the 3D inversion of AEM data acquired for salinity mapping over the Bookpurnong Irrigation District in South Australia. We have inverted 146 line km of RESOLVE data for a 3D conductivity model with ~310 000 elements in 45 min using just five processors of a multi-processor workstation.
Thermoelectric properties of Bi2Te3 disk fabricated from rice kernel-like Bi2Te3 powder

Rice kernel (RK)-like bismuth telluride (Bi2Te3) crystals were successfully synthesised by microwave-induced plasma heating of Bi and Te powders. Phase and morphology characterisation revealed the presence of the Bi2Te3 structure in the shape of RKs. The crystal orientation factor (f value) of RK Bi2Te3 powder was larger than that of the RK Bi2Te3 hot-pressed disk. A comparison of the f values of both samples suggested that the RK shape has significant influence in reducing the f value after hot processing. The Seebeck coefficient (S), electrical resistivity (ρ) and thermal conductivity (κ) of the RK Bi2Te3 disk were determined over the temperature ranging from 323 to 623 K. The S value was negative over the whole temperature range, indicating an n-type thermoelectric RK Bi2Te3 disk. The power factor (S 2 ρ −1) was the highest at about 1.07 × 10−3 W/m K2 at 323 K and decreased with increasing temperature. The maximum dimensionless figure of merit (ZT) of the RK Bi2Te3 disk was 0.26 at about 366 K.
Intake, digestion, and nitrogen utilization by sheep fed tropical legumes with contrasting tannin concentration and astringency.

We conducted an experiment to determine the effects of concentration and astringency of extractable and bound condensed tannins (CT) in tropical legumes on intake, digestibility, and nitrogen (N) utilization by sheep. The test legumes (Desmodium ovalifolium and Flemingia macrophylla) had similar concentrations of extractable CT (90 g/kg DM) but different concentrations of bound CT and astringency of tannins. Chopped, sun-dried forage of each legume was sprayed with either water (control) or polyethylene glycol (PEG, 35 g/kg of DM) to bind extractable CT and fed daily (26 g/kg BW) to eight sheep with ruminal and duodenal cannulas. The sheep also received starch-extracted cassava meal intraruminally (4 g/kg BW) as a constant source of readily fermentable carbohydrates. Intake of the two legumes was not different (P > .05), but it increased an average of 10% (P < .01) when extractable CT were reduced from 90 to 50 g/kg of DM with PEG. Ruminal and total tract digestibilities of OM, NDF, and ADF were greater (P < .01) with D. ovalifolium than with F. macrophylla and increased for both legumes with the addition of PEG. Greater (P < .01) N flow to the duodenum, N absorbed from the intestine, and fecal N were observed with F. macrophylla than with D. ovalifolium. Extraction of CT with PEG resulted in less (P < .05) ruminal escape protein and less (P < .01) fecal N with both legumes, but apparent postruminal N digestion was not affected. Changes in the concentration of extractable CT in tropical legumes can significantly affect forage intake, digestion, and N utilization by sheep.
A novel class of Pseudoautosomal region 1 deletions downstream of SHOX is associated with Leri-Weill dyschondrosteosis.

Leri-Weill dyschondrosteosis (LWD) is a pseudoautosomal dominant disorder characterized by disproportionate short stature and a characteristic curving of the radius, known as the "Madelung deformity. " SHOX mutations resulting in SHOX haploinsufficiency have been found in LWD and in a variable proportion of patients with idiopathic short stature (ISS), whereas homozygous loss of SHOX results in the more severe Langer mesomelic dysplasia (LMD). Defects in SHOX have been identified in approximately 60% of LWD cases, whereas, in the remaining approximately 40%, the molecular basis is unknown. This suggests either genetic heterogeneity or the presence of mutations in unanalyzed regions of SHOX, such as the upstream, intragenic, or downstream regulatory sequences. Therefore, the pseudoautosomal region 1 (PAR1) of 80 patients with LWD, in whom SHOX deletions and mutations had been excluded, was screened for deletions by use of a new panel of microsatellite markers. We identified 12 patients with LWD who presented with a novel class of PAR1 deletions that did not include SHOX. The deletions were of variable size and mapped at least approximately 30-530 kb downstream of SHOX. In our cohort, this type of deletion accounted for 15% of cases. In all cases, the deletions cosegregated with the phenotype. No apparent phenotypic differences were observed between patients with SHOX deletions and those with this new class of PAR1 deletions. Thus, we present here the identification of a second PAR1 region implicated in the etiopathogenesis of LWD. Our findings suggest the presence of distal regulatory elements of SHOX transcription in PAR1 or, alternatively, the existence of an additional locus apparently involved in the control of skeletal development. Deletion analysis of this newly identified region should be included in the mutation screening of patients with LWD, LMD, and ISS.