Miracle-dz/UniFAR-FTUs huggingface dataset:
Redox Control of the DNA Damage-inducible Protein DinG Helicase Activity via Its Iron-Sulfur Cluster*

The Escherichia coli DNA damage-inducible protein DinG, a member of the superfamily 2 DNA helicases, has been implicated in the nucleotide excision repair and recombinational DNA repair pathways. Combining UV-visible absorption, EPR, and enzyme activity measurements, we demonstrate here that E. coli DinG contains a redox-active [4Fe-4S] cluster with a midpoint redox potential (Em) of –390 ± 23 mV (pH 8.0) and that reduction of the [4Fe-4S] cluster reversibly switches off the DinG helicase activity. Unlike the [4Fe-4S] cluster in E. coli dihydroxyacid dehydratase, the DinG [4Fe-4S] cluster is stable, and the enzyme remains fully active after exposure to 100-fold excess of hydrogen peroxide, indicating that DinG could be functional under oxidative stress conditions. However, the DinG [4Fe-4S] cluster can be efficiently modified by nitric oxide (NO), forming the DinG-bound dinitrosyl iron complex with the concomitant inactivation of helicase activity in vitro and in vivo. Reassembly of the [4Fe-4S] cluster in NO-modified DinG restores helicase activity, indicating that the iron-sulfur cluster in DinG is the primary target of NO cytotoxicity. The results led us to propose that the iron-sulfur cluster in DinG may act as a sensor of intracellular redox potential to modulate its helicase activity and that modification of the iron-sulfur cluster in DinG and likely in other DNA repair enzymes by NO may contribute to NO-mediated genomic instability.
Bioengineered cartilage in a scaffold-free method by human cartilage-derived progenitor cells: a comparison with human adipose-derived mesenchymal stromal cells.

The objective of our study was to investigate chondrogenesis potential of human adipose-derived mesenchymal stromal cells (MSCs), using as a positive control a human source of cartilage-derived progenitor cells (PCs). This source of PCs was recently described by our group and dwells on the surface of nasoseptal cartilage. Histological analysis using Safranin O staining and immunofluorescence for actin filaments and collagen type II was performed on three-dimensional (3D) pellet cultures. Cartilage PCs and adipose MSCs showed similarities in monolayer culture related to cell morphology and proliferation. Our 3D pellet cultures substantially reduced the actin stress and after 21 days under chondrogenic medium, we observed an increase in the pellet diameter for cartilage PCs (7.4%) and adipose MSCs (21.2%). Adipose-derived MSCs responded to chondrogenic stimulus, as seen by positive areas for collagen type II, but they were not able to recreate a mature extracellular matrix. Using semi-quantitative analysis, we observed a majority of Safranin O areas rising from blue (no stain) to orange (moderate staining) and no changes in fibroblastic morphology (P < 0.0001). For cartilage PCs, chondrogenic induction is responsible for morphological changes and a high percentage of matrix area/number of cells (P ≤ 0.0001), evaluated by computerized histomorphometry. Morphological analyses reveal that adipose-derived MSCs were not able to recreate a bioengineered cartilage. The cost of culture was reduced, as the cartilage PCs under growth-factor free medium exhibit a high score for cartilage formation compared with the induced adipose mesenchymal stromal cells (P = 0.0021). Using a pellet 3D culture, our cartilage PCs were able to produce a cartilage tissue in vitro, leading to the future development of bioengineered products.
Semirna: searching for plant miRNAs using target sequences.

Many plant genomes are already known, and new ones are being sequenced every year. The next step for researchers is to identify all of the functional elements in these genomes, including the important class of functional elements known as microRNAs (miRNAs), which are involved in posttranscriptional regulatory pathways. However, computational tools for predicting new plant miRNAs are limited, and there is a particular need for tools that can be used easily by laboratory researchers. We present semirna, a new tool for predicting miRNAs in plant genomes, available as a Web server. This tool takes a putative target sequence such as a messenger RNA (mRNA) as input, and allows users to search for miRNAs that target this sequence. It can also be used to determine whether small RNA sequences from massive sequencing analysis represent true miRNAs and to search for miRNAs in new genomes using homology. Semirna has shown a high level of accuracy using various test sets, and gives users the ability to search for miRNAs with several different adjustable parameters. Semirna, a user-friendly and intuitive Web server for predicting miRNA sequences, can be reached at http://www.bioinfocabd. upo.es/semirna/ . It is useful for researchers searching for miRNAs involved in particular pathways, as well as those searching for miRNAs in newly sequenced genomes.
Tris(1,10-phenanthrolin-1-ium) hexacyanidoferrate(III) ethanol monosolvate trihydrate

The asymmetric unit of the title complex, (C12H9N2)3[Fe(CN)6]·C2H5OH·3H2O, consists of two half [Fe(CN)6]3− anions located on inversion centers, three 1,10-phenanthrolin-1-ium cations, [Hphen]+, an ethanol and three water solvent molecules. The average Fe—C and C—N bond lengths are 1.942 (6) and 1.154 (3) Å, respectively, while the Fe—C—N angles deviate slightly from linearity with values ranging from 177.8 (2) to 179.7 (2)°. The FeIII atoms adopt a distorted octahedral geometry. All the species are linked through O—H⋯N, N—H⋯O and O—H⋯O hydrogen-bonding interactions, resulting in a three-dimensional supramolecular network.
Possession Experiences in Dissociative Identity Disorder: A Preliminary Study

Dissociative trance disorder, which includes possession experiences, was introduced as a provisional diagnosis requiring further study in the Diagnostic and Statistical Manual of Mental Disorders (4th ed.). Consideration is now being given to including possession experiences within dissociative identity disorder (DID) in the Diagnostic and Statistical Manual of Mental Disorders (5th ed.), which is due to be published in 2013. In order to provide empirical data relevant to the relationship between DID and possession states, I analyzed data on the prevalence of trance, possession states, sleepwalking, and paranormal experiences in 3 large samples: patients with DID from North America; psychiatric outpatients from Shanghai, China; and a general population sample from Winnipeg, Canada. Trance, sleepwalking, paranormal, and possession experiences were much more common in the DID patients than in the 2 comparison samples. The study is preliminary and exploratory in nature because the samples were not matched in any way.
Heparin Structure and Interactions with Basic Fibroblast Growth Factor

Crystal structures of heparin-derived tetra- and hexasaccharides complexed with basic fibroblast growth factor (bFGF) were determined at resolutions of 1.9 and 2.2 angstroms, respectively. The heparin structure may be approximated as a helical polymer with a disaccharide rotation of 174° and a translation of 8.6 angstroms along the helix axis. Both molecules bound similarly to a region of the bFGF surface containing residues asparagine-28, arginine-121, lysine-126, and glutamine-135; the hexasaccharide also interacted with an additional binding site formed by lysine-27, asparagine-102, and lysine-136. No significant conformational change in bFGF occurred upon heparin oligosaccharide binding, which suggests that heparin primarily serves to juxtapose components of the FGF signal transduction pathway.
Thromboelastometry: Relation to the severity of liver cirrhosis in patients considered for liver transplantation

Abstract The severity of liver disease is assessed by scoring systems, which include the conventional coagulation test prothrombin time-the international normalized ratio (PT-INR). However, PT-INR is not predictive of bleeding in liver disease and thromboelastometry (ROTEM) has been suggested to give a better overview of the coagulation system in these patients. It has now been suggested that coagulation as reflected by tromboelastomety may also be used for prognostic purposes. The objective of our study was to investigate whether thrombelastometry may discriminate the degree of liver insufficiency according to the scoring systems Child Pugh and Model for End-stage Liver Disease (MELD). Forty patients with chronic liver disease of different etiologies and stages were included in this observational cross-sectional study. The severity of liver disease was evaluated using the Child-Pugh score and the MELD score, and blood samples for biochemistry, conventional coagulation tests, and ROTEM were collected at the time of the final assessment for liver transplantation. Statistical comparisons for the studied parameters with scores of severity were made using Spearman correlation test and receiver-operating characteristic (ROC) curves. Spearman correlation coefficients indicated that the thromboelastometric parameters did not correlate with Child-Pugh or MELD scores. The ROC curves of the thromboelastometric parameters could not differentiate advanced stages from early stages of liver cirrhosis. Standard ROTEM cannot discriminate the stage of chronic liver disease in patients with severe chronic liver disease.
System impact of pulsed power loads on a laboratory scale integrated fight through power (IFTP) system

Pulsed power weaponry is being considered for inclusion in future warships. In this work, the effects of pulsed power weaponry on a power distribution and propulsion system are demonstrated in the context of a physical system known as the naval combat survivability testbed. It is shown that, as expected, when using an integrated fight through power (IFTP) architecture, the pulsed power load results in a disturbance on the generation ac bus; but it has no effect on the zonal ac busses. The use of propulsion coordination is also investigated.
Development of fish-like boid simulator based on biological code of behavior

This paper discuss boid simulation using the rules of biological behavior to estimate fish behavior. The modeling and computational algorithm are cheched with validity under chaos and fractal analysis. Our simulation method for sensing and acting of a fish is based on the boid method in conjunction with multi agent system. The fish-like boid rules are extracted from the various real fish behavior in water tank experiment. The estimation method for complexities of the fish locomotive behavior are based on the chaos and fractal theories. We can show the comparison of computational results and experimental one throught the chaos and fractal analysis.
Dendritic trafficking of BDNF mRNA is mediated by translin and blocked by the G196A (Val66Met) mutation

Alternatively spliced brain-derived neurotrophic factor (BDNF) transcripts are targeted to distinct cellular compartments in neurons but the mechanisms underlying this sorting are unknown. Although only some BDNF isoforms are targeted to dendrites, we have found that the coding region common to all BDNF transcripts contains a constitutively active dendritic targeting signal and that this signal is suppressed in transcripts containing exons 1 or 4, which are restricted to the cell soma and proximal dendrites. This dendritic targeting signal is mediated by translin, an RNA-binding protein implicated in RNA trafficking, and is disrupted by the G196A mutation associated with memory deficits and psychiatric disorders. Molecular modeling and mutational studies indicate that the G196A mutation blocks dendritic targeting of BDNF mRNA by disrupting its interaction with translin. These findings implicate abnormal dendritic trafficking of BDNF mRNA in the pathophysiology of neuropsychiatric disorders linked to the G196A mutation.
Marginal bone loss in implants placed in grafted maxillary sinus.

PURPOSE The purpose of this study is to evaluate the vertical and horizontal graft bone resorption (GR) in grafted maxillary sinuses and the marginal bone loss (MBL) around implants placed in the sinuses with different prosthetic connections and to determine the effect of other clinical factors on these tissue responses at 6 and 18 months postloading. MATERIAL AND METHOD A total of 254 implants were placed in 150 grafted maxillary sinuses of 101 patients (51.5% female) with mean age of 52.2 years (range, 32-82 years). GR and MBL measurements were made in implants placed with two different prosthetic connections (internal and external) at 6 and 18 months postloading. The complex samples general linear model was used to analyze the influence of patient age, gender, smoking habit, history of periodontal disease, implantation timing (simultaneous vs deferred), and prosthetic abutment length on radiographic GR and MBL values. RESULTS At 18 months postloading, the MBL ranged from 0 mm to 5.89 mm; less than 1 mm was lost around 49.0% (mesial) and 44.3% (distal) of the implants, while no bone was lost around 32.9% (mesial) and 26.7% (distal). The GR was significantly affected by smoking, remnant alveolar bone height, graft length, graft height, gender, and age, and it significantly decreased over time. The MBL was influenced by the type of connection, implantation timing, and prosthetic abutment length. The MBL was greater with longer postloading interval and higher patient age and in smokers. CONCLUSION Resorption of grafts that combine autogenous cortical bone with anorganic bovine bone is dependent on the anatomic features of the sinus and is not affected by the time elapsed after the first 6 months. The MBL in implants placed in these grafted areas is time dependent and mainly related to potentially modifiable clinical decisions and patient habits.
Substance Use Among High School Athletes

SUMMARY During the past two decades, prevention specialists have responded to concerns about youthful substance use by developing a variety of programs. The most effective of these programs have been based upon our understanding of the risk and protective factors involved. While student-athletes generally share the same level of risk as other high school students, as a group, they may have other characteristics that can be considered. In addition, the special socializing experience of participating in athletics may present special opportunities for prevention. We suggest that it is prudent to build upon important lessons in designing programs for student athletes and we provide, as a starting point, an overview of twelve key processes with demonstrated impact.
Liana Impacts on Carbon Cycling, Storage and Sequestration in Tropical Forests

Mature tropical forests sequester large quantities of atmospheric CO2, which they store as plant biomass. These forests are changing however, including an increase in liana abundance and biomass over recent decades in Neotropical forests. We ask here how this increase in lianas might impact the tropical forest carbon cycle and their capacity for carbon storage and sequestration. Lianas reduce tree growth, survival, and leaf productivity; however, lianas also invest significantly in leaf production, and the increase in lianas could conceivably offset liana‐induced reductions in tree canopy productivity with no adverse effects to the forest‐level canopy productivity. By contrast, lianas decrease the total ecosystem uptake of carbon by reducing tree biomass productivity. Lianas themselves invest little in woody biomass, and store and sequester only a small proportion of the biomass in tropical forests. As lianas increase they may effectively displace trees, but the greater liana carbon stocks are unlikely to compensate for liana‐induced losses in net carbon sequestration and storage by trees. A potentially important additional consideration is the impact of lianas on the tree community. By competing more intensely with shade‐tolerant, more densely wooded trees than with fast‐growing, light‐wooded trees, lianas may shift tree composition toward faster‐growing species, which store relatively little carbon, and thereby further reduce the carbon storage capacity of tropical forests. Overall, current evidence indicates that the increase in lianas will negatively impact the carbon balance of tropical forests, with potentially far‐reaching consequences for global atmospheric CO2 levels and associated climate change.
Evaluation of an Axial Pattern Flap Based on the Cranial Cutaneous Branch of the Saphenous Artery: A Cadaveric Perfusion Study.

OBJECTIVES To confirm the anatomic location of the cranial cutaneous branch of the saphenous artery (CCSA), delineate the angiosome of the CCSA, and provide guidelines for clinical use of an axial pattern flap based on the CCSA. STUDY DESIGN Anatomic study. ANIMALS Greyhound cadavers (n=10). METHODS Shortly after euthanasia, the CCSA was identified and isolated in each hindlimb. Methylene blue and radiographic perfusion studies were performed. The skin was freed from the thigh for photographic and radiographic images. The dimensions of the skin area suitable for use as an axial pattern flap were related to anatomical landmarks. Mock surgical elevation and transposition of the flap in 2 dogs allowed assessment of flap mobility and ease of donor site closure for clinical use. RESULTS The CCSA was reliably identified in all dogs branching from the saphenous artery as it became superficial to the sartorius muscle, immediately distal to the caudal cutaneous branch and proximal to the genicular branches. Genicular branches were variably paired or singular. Perfusion studies defined the CCSA angiosome as the area cranial to the saphenous artery and caudal to the cranial border of the thigh, extending proximally from the level of the medial tibial condyle to two-thirds of the distance to the inguinal ring. CONCLUSION An axial pattern flap based on the CCSA could be expected to cover skin defects of the cranial aspect of the distal thigh and stifle, the popliteal region caudal to the stifle, and the proximal medial crus.
Calculation of Molecular Configuration Integrals

A method is presented for calculating the conformational free energy of a molecule in all degrees of freedom. The method uses the harmonic approximation with finite integration ranges, along with Mode Scanning, a fast correction for anharmonicity based upon internal bond-angle-torsion coordinates. Mode Scanning accounts for local anharmonicity without the need for expensive Monte Carlo integration. The method is efficient, and comparisons with analytic or highly detailed numerical calculations show excellent accuracy. Similar comparisons for the previously described Mode Integration method show that, although it is computationally demanding, it can be less accurate than the pure harmonic approximation. The inaccuracy of Mode Integration is traceable to its use of a Cartesian coordinate basis set; much more accurate results are obtained when the basis set consists of bond-angle-torsion coordinates.
Elevated expression of CCL5/RANTES in adult T‐cell leukemia cells: Possible transactivation of the CCL5 gene by human T‐cell leukemia virus type I tax

HTLV‐I is the etiologic agent of ATL and of tropical spastic paraparesis/HTLV‐I‐associated myelopathy. Infiltration of various tissues by circulating leukemic cells and HTLV‐I‐infected T cells is a characteristic of ATL and HTLV‐I‐associated inflammatory diseases. Chemokines play important roles in migration and tissue localization of various lymphocyte subsets. Here, we report the highly frequent expression of CCL5 (RANTES) in ATL and HTLV‐I‐infected T‐cell lines. Among various human T‐cell lines, those infected with HTLV‐I selectively expressed the CCL5 gene and secreted CCL5. Furthermore, CCL5 was expressed by leukemic cells in peripheral blood and lymph nodes from patients with ATL. Inducible expression of HTLV‐I transcriptional activator Tax in a human T‐cell line Jurkat, up‐regulated CCL5 mRNA and induced CCL5 secretion. Analysis of the CCL5 promoter revealed that this gene is activated by Tax, via the activation of NF‐κB, whose responsive element, R(A/B), is located at positions −71 to −43 relative to the putative transcription start site. Aberrant expression of CCL5 by HTLV‐I‐infected T cells may impact on the pathophysiology of HTLV‐I‐associated diseases. © 2004 Wiley‐Liss, Inc.
Optical conductivity in high-Tc superconductors.

The optical conductivity of a superconductor with arbitrary mean free path is calculated with use of an imaginary-frequency formulation. We obtain good agreement with the results of a recent real-axis formulation and, in most cases, with another imaginary-frequency formulation. Extending the work to a simple version of a recently proposed phenomenological charge-transfer resonance model for the CuO, it is found that in the clean limit the absorption will start at four times the gap ({Delta}{sub 0}) while introducing impurities produces absorption starting at twice {Delta}{sub 0}. In agreement with experiment, strong coupling effects at higher energies need not be large in this model.
An improved direct inverse modeling approach for high-speed feedforward tracking control of a piezoelectric tube actuator

To enhance the performance for high-speed tracking control of a piezoelectric tube actuator (PTA), an improved direct inverse rate-dependent PI model is obtained in this paper, and then adopted to design a practical feedforward controller achieving high-speed tracking control for a high-frequency trajectory with strong robustness. Specifically, based on the Prandtl-Ishlinskii (PI) model, an improved direct rate-dependent inverse model is set up for the PTA, with a polynomial function module introduced to eliminate the influence caused by the structure nonlinearity. Then, considering the features of the PTA structure, some preprocessing procedure is proposed to handle the collected experimental data, with the results utilized to identify all the unknown parameters over a wide bandwidth. Based on the obtained model, a practical feedforward controller, which presents the advantages of high-speed response, simple structure and convenient implementation, is then designed to enable the PTA to track high-frequency trajectories with satisfactory precision. Some experimental results are provided, which clearly demonstrate the high precision of the constructed/identified model, and the satisfactory performance of the proposed practical feedforward tracking control law.
A Novel Dopamine Receptor Signaling Unit in Brain: Heterooligomers of D1 And D2 Dopamine Receptors

The ability of G protein coupled receptors to heterooligomerize and create novel signaling complexes has demonstrated the tremendous potential of these receptors to access diverse signaling cascades, as well as to modulate the nature of the transduced signal. In the dopamine receptor field, the existence of a D1-like receptor in brain that activated phospatidylinositol turnover has been shown, but definition of the molecular entity remained elusive. We discovered that the D1 and D2 receptors form a heterooligomer, which on activation of both receptors, coupled to Gq to activate phospholipase C and generate intracellular calcium release. The activation of Gq by the D1-D2 heterooligomer has been shown to occur in cells expressing both receptors, as well as in striatum, distinct from Gs/olf or Gi/o activation by the D1 and D2 receptor homooligomers, respectively. The activation of the D1-D2 receptor heterooligomer in brain led to a calcium signal–mediated increase in phosphorylation of calmodulin kinase lla. The calcium signal rapidly desensitized and the receptors cointernalized after occupancy of either the D1 or D2 binding pocket. Thus, the D1-D2 heterooligomer directly links the action of dopamine to rapid calcium signaling and likely has important effects on dopamine-mediated synaptic plasticity and its functional correlates in brain.