Miracle-dz/UniFAR-FTUs huggingface dataset:
Crystal structure and novel recognition motif of rho ADP-ribosylating C3 exoenzyme from Clostridium botulinum: structural insights for recognition specificity and catalysis.

Clostridium botulinum C3 exoenzyme inactivates the small GTP-binding protein family Rho by ADP-ribosylating asparagine 41, which depolymerizes the actin cytoskeleton. C3 thus represents a major family of the bacterial toxins that transfer the ADP-ribose moiety of NAD to specific amino acids in acceptor proteins to modify key biological activities in eukaryotic cells, including protein synthesis, differentiation, transformation, and intracellular signaling. The 1.7 A resolution C3 exoenzyme structure establishes the conserved features of the core NAD-binding beta-sandwich fold with other ADP-ribosylating toxins despite little sequence conservation. Importantly, the central core of the C3 exoenzyme structure is distinguished by the absence of an active site loop observed in many other ADP-ribosylating toxins. Unlike the ADP-ribosylating toxins that possess the active site loop near the central core, the C3 exoenzyme replaces the active site loop with an alpha-helix, alpha3. Moreover, structural and sequence similarities with the catalytic domain of vegetative insecticidal protein 2 (VIP2), an actin ADP-ribosyltransferase, unexpectedly implicates two adjacent, protruding turns, which join beta5 and beta6 of the toxin core fold, as a novel recognition specificity motif for this newly defined toxin family. Turn 1 evidently positions the solvent-exposed, aromatic side-chain of Phe209 to interact with the hydrophobic region of Rho adjacent to its GTP-binding site. Turn 2 evidently both places the Gln212 side-chain for hydrogen bonding to recognize Rho Asn41 for nucleophilic attack on the anomeric carbon of NAD ribose and holds the key Glu214 catalytic side-chain in the adjacent catalytic pocket. This proposed bipartite ADP-ribosylating toxin turn-turn (ARTT) motif places the VIP2 and C3 toxin classes into a single ARTT family characterized by analogous target protein recognition via turn 1 aromatic and turn 2 hydrogen-bonding side-chain moieties. Turn 2 centrally anchors the catalytic Glu214 within the ARTT motif, and furthermore distinguishes the C3 toxin class by a conserved turn 2 Gln and the VIP2 binary toxin class by a conserved turn 2 Glu for appropriate target side-chain hydrogen-bonding recognition. Taken together, these structural results provide a molecular basis for understanding the coupled activity and recognition specificity for C3 and for the newly defined ARTT toxin family, which acts in the depolymerization of the actin cytoskeleton. This beta5 to beta6 region of the toxin fold represents an experimentally testable and potentially general recognition motif region for other ADP-ribosylating toxins that have a similar beta-structure framework.
Research of Image Matching Based on Improved SURF Algorithm

In the study, it presents an efficient algorithm based on SURF (Speeded Up Robust Features). The method applies the SURF algorithm in the detection and description for image features, first it applies the SURF feature detector in extracting reference images and matching feature points in the image, respectively, then it uses DAISY algorithm instead of the SURF algorithm to calculate the character description of each feature point vector. In the process of feature points matching, the false matching points are eliminated through RANSAC algorithm. Finally, according to the rest of the match point, it can estimate the space geometric transformation parameters between two images and thus matching process is completed. DOI : http://dx.doi. org/10.11591/telkomnika.v12i2. 3951
Learning to play like a human: case injected genetic algorithms for strategic computer gaming

We use case injected genetic algorithms to learn how to competently play computer strategy games. Strategic computer games involve long range planning across complex dynamics and imperfect knowledge presented to players requires them to anticipate opponent moves and adapt their strategies accordingly. This work addresses the problem of acquiring and using knowledge from human players for such games. Specifically, we learn general routing information from a human player and use case-injected genetic algorithms to incorporate this acquired knowledge in subsequent planning. Results from a strike planning game show that with an appropriate representation, case injection effectively biases the genetic algorithm toward producing plans that contain important strategic elements used by human players.
Cellular mechanisms of acute and chronic adaptation of rat renal P(i) transporter to alterations in dietary P(i).

Recently, the cDNA for a Na-P(i) cotransport system of rat kidney cortex (NaPi-2) has been identified by expression cloning. Using polyclonal antibodies raised against this renal Na-P(i) cotransport system, and using the polymerase chain reaction after reverse transcription of mRNA in microdissected nephron segments, we recently demonstrated that NaPi-2-related mRNA and protein is expressed in the brush-border membranes (BBM) of the proximal tubules of rat kidney. The purpose of the present study was to study the cellular mechanisms involved in adaptation of rat renal Na-P(i) cotransporter to acute and chronic alterations in dietary P(i). Compared with rats fed chronically (7 days) a high-P(i) diet (1.2%), in rats fed chronically a low-P(i) (0.1%) diet the 3.4-fold increase in BBM Na-P(i) cotransport rate (chronic upregulation) was associated with a 2.2-fold increase in renal cortical NaPi-2 mRNA and a 4.9-fold increase in BBM NaPi-2 protein abundances. In contrast, compared with rats fed chronically (7 day) a high-P(i) diet, in rats fed acutely (2 h) a low-P(i) diet the 1.5-fold increase in Na-P(i) cotransport rate (acute upregulation) was associated with a 1.8-fold increase in NaPi-2 protein but no change in NaPi-2 mRNA abundance. Similarly, compared with rats fed chronically a low-P(i) diet, in rats fed acutely (2 h) a high-P(i) diet the 1.9-fold decrease in Na-P(i) cotransport rate (acute downregulation) was associated with a 3.8-fold decrease in NaPi-2 protein but no change in NaPi-2 mRNA abundance. (ABSTRACT TRUNCATED AT 250 WORDS)
Prefactual Potency

Prefactual thoughts typically take the form of implied or explicit if–then statements that represent mental simulations of alternatives to what is expected to occur in the future. The authors propose that the multiplicative combination of “if likelihood” (the degree to which the antecedent condition of the prefactual is perceived to be likely) and “then likelihood” (the perceived conditional likelihood of the outcome of the prefactual, given the antecedent condition) determine the influence of prefactuals. This construct, termed prefactual potency, is a reliable predictor of the degree of influence of prefactual thinking on judgments of anticipated negative affect. Through three experiments, the authors demonstrate the predictive power of this construct and show that it plays a causal role in determining the strength of the effects of prefactual thought. Implications of prefactual potency as a central factor of prefactual influence are discussed.
A Comparative Survey the Effect of Education Based program on Health Belief Model for the Use Osteoporosis Preventive Behaviors of the Girl ’ s Osteoporotic and non-Osteoporotic Mothers

Osteoporosis is a global health issue along with heart disease, stroke, diabetes and cancer and takes up many financial resources for prevention and treatment. It affects more than 75 million people worldwide. So the purpose of this study was to examine comparative survey the effect of education based program of health belief model on the use osteoporosis preventive behaviors the girls of osteoporotic and non-osteoporotic mothers. This study is a quasiexperimental research with two groups trial (n= 42) and control (n=41) in Kerman in May to December of 2012. Data collection tools include demographic information, health belief model scale, calcium intake and sport self-report checklist. That demographic information, health belief model scale completed with mothers and self-reports checklist completed with their girls. For analyzing data used SPSS16 software (descriptive statistics, paired t-test, Man-Witney U, repeated measures and Wilcoxon). About health belief model of mothers in trial group, between before and after intervention tests showed significant difference in perceived benefits of calcium intake (p=0.03) and sport (P=0.004), barriers of calcium intake(P=0/00) and sport (P=0/00). About calcium intake (P=0/00) and time of sport (P=0/00) in girls statistical analysis showed a significant difference before and 1 and 3 months after intervention. The comparison between osteoporotic and non-osteoporotic mother's, before and after intervention for calcium intake and sport shows no significant difference (P>0.05). As regards that educational program have a significant effect in using osteoporosis preventive behaviors, planning interventions have an important role for increasing knowledge of mothers and their girls and changing their behavior.
Cognitive reserve as a moderator of the negative association between mood and cognition: evidence from a population-representative cohort

Background Cognitive reserve (CR) has been associated with better cognitive function and lower risk of depression in older people, yet it remains unclear whether CR moderates the association between mood and cognition. This study aimed to investigate whether a comprehensive indicator of CR, including education, occupation and engagement in cognitive and social activities, acts as a moderator of this association. Methods This was a cross-sectional study utilising baseline data from the Cognitive Function and Ageing Study II (CFAS II), a large population-based cohort of people aged 65+ in England. Complete data on the measures of CR, mood and cognition were available for 6565 dementia-free individuals. Linear regression models were used to investigate the potential modifying effect of CR on the association between cognition and mood with adjustment for age, sex and missing data. Results Levels of CR did moderate the negative association between mood and cognition; the difference in cognition between those with and without a clinical level mood disorder was significantly smaller in the middle (−2.28; 95% confidence interval (CI) −3.65 to −0.90) and higher (−1.30; 95% CI −2.46 to −0.15) CR groups compared with the lower CR group (−4.01; 95% CI −5.53 to −2.49). The individual components of CR did not significantly moderate the negative association between mood and cognition. Conclusion These results demonstrate that CR, indexed by a composite score based on multiple indicators, can moderate the negative association between lowered mood and cognition, emphasising the importance of continuing to build CR across the lifespan in order to maintain cognitive health.
RNA polymerase: structural similarities between bacterial RNA polymerase and eukaryotic RNA polymerase II.

Bacterial RNA polymerase and eukaryotic RNA polymerase II exhibit striking structural similarities, including similarities in overall structure, relative positions of subunits, relative positions of functional determinants, and structures and folding topologies of subunits. These structural similarities are paralleled by similarities in mechanisms of interaction with DNA.
Separation and partial characterization of the enzymes of the toluene-4-monooxygenase catabolic pathway in Pseudomonas mendocina KR1

The route of toluene degradation by Pseudomonas mendocina KR1 was studied by separating or purifying from toluene-grown cells the catabolic enzymes responsible for oxidation of p-cresol through the ring cleavage step. Enzymatic transformations corresponding to each of the metabolic steps in the proposed degradative pathway were conducted with cell-free preparations. p-Cresol was metabolized by the enzyme p-cresol methylhydroxylase to p-hydroxybenzaldehyde. p-Hydroxybenzaldehyde was further oxidized by partially purified enzyme preparations to p-hydroxybenzoate and subsequently hydroxylated to form protocatechuate. Protocatechuate was then oxidized by ortho ring cleavage.
Comprehensive progressive decoding for JPEG compressed image

The explosive growth of images and videos on the World Wide Web (WWW) is making the Web into a huge resource of visual information. Among various types of multimedia information, still images or dynamic images (video clips) in compressed format are the most widely accepted on the WWW. Therefore, it becomes an essential issue to achieve the maximum efficiency in transmitting and decoding those compressed images on the Internet. Progressive coding provides a mode that allows a coarse version of an image being transmitted at a lower bit rate and then gradually refined by subsequent transmissions. Compared with conventional coding, it is more suitable for interactive applications such as those involving JPEG images on the Internet. In this paper, we first give an approximation of cosine function used in IDCT for the various orders. Based on the approximation and a series analysis, we then develop a progressive decoding scheme which comprehends the successive approximation and the spectral selection. The analysis and experiments establish the fact that our proposed method saves computational cost significantly in comparison with the existing spectral selection based progressive decoding proposed by JPEG. Extensive experiments are carried out to evaluate the proposed algorithm, which reveals that, the reconstructed images, even at the lowest bit rate and with lower order approximation, can still achieve encouraging PSNR values.
Stereotactic biopsy of brainstem lesions: Techniques, efficacy, safety, and disease variation between adults and children: A single institutional series and review

Background: Stereotactic biopsy of brainstem lesions have been performed with varying indications, with most of the literature reporting on children. Materials and Methods: The present study retrospectively analyzed all cases that underwent stereotactic biopsy for brainstem lesion in both adult and pediatric population between 1994 and 2009 in a single tertiary neurosurgical center. The clinical and radiological features, technique of the procedure, morbidity, diagnostic accuracy, spectrum of diagnosis, and variations in adult and pediatric population were analyzed. Results: Eighty-two patients were included in the study. Computed tomography (CT) was used as guidance in 73 (38 children and 35 adults) patients and magnetic resonance imaging (MRI) in 9 (3 children and 6 adults). The biopsy was performed in a procedure room under local anesthesia in most adults, while children required sedation. Glioblastoma comprised 29.3% of all pathologies in children, compared with only 4.9% of the pathologies in adult population (P = 0.007). Tuberculosis was the next major diagnosis (9.8%). In 12 patients, initial biopsy was inconclusive. Following a repeat biopsy in 5 of these patients, a diagnosis was possible for 75/82 (91.5%) patients by STB. The location of the target, the choice of entry, the radiological characteristic of the lesion, enhancement pattern, and age group did not significantly correlate with the occurrence of inconclusive biopsy. Permanent complications occurred in two patients (2.4%). There was no mortality in this series. Conclusion: Stereotactic biopsy has an important role in brainstem lesions, more significantly in adults, due to wider pathological spectrum. It can be performed safely under local anesthesia through a twist drill craniostomy in most of the adults.
Ambiguity function analysis for OFDM radar signals

Orthogonal Frequency Division Multiplexing (OFDM) is an efficient modulation method which is widely used in many mobile communication systems. Applying OFDM signals to radar systems will make the combination of radar and communication systems in one single system platform possible. In this paper, the auto-correlation and cross-correlation components of the ambiguity function are researched for the analysis of the performance of the OFDM signal resolution. The impact of sparse subcarriers on the resolution of the delay and the Doppler is also discussed. Finally, the conclusions are verified.
Roles of reinforced nerve conduits and low-level laser phototherapy for long gap peripheral nerve repair

Peripheral nerve injuries are common in clinical practice because of traumas such as crushing and sectioning. Lesions of the nerve structure result in lost or diminished sensitivity and/or motor activity in the innervated territory. The degree of lesion depends on the specific nerve involved, the magnitude and type of pressure exerted, and the duration of the compression. The results of such injuries commonly include axonal degeneration and retrograde degeneration of the corresponding neurons in the spinal medulla, followed by very slow regeneration (Rochkind et al., 2001). The adverse effects on the daily activities of patients with a peripheral nerve injury are a determining factor in establishing the goals of early recovery (Rodriguez et al., 2004). The most severe form of nerve damage involves complete transection of the nerve, which results in the loss of sensory and motor function at the site of injury. Although a degree of recovery can be expected in most untreated nerve injuries, the process is slow and often incomplete. Moreover, despite considerable advances in microsurgical techniques, the functional results of peripheral nerve repair remain largely unsatisfactory. The regrowth of nerves across large gaps is particularly challenging, usually requiring a nerve graft to correctly bridge the proximal and distal nerve stumps. At present, nerve autografting is the most common treatment used to repair peripheral nerve defects. However, this recognized “gold standard” technique has a number of inherent disadvantages, such as limited availability of donor tissue (IJkema-Paassen et al., 2004), secondary deformities, potential differences in tissue structure and size (Nichols et al., 2004), and numbness at donor sites (Bini et al., 2004). Although xenografts and allografts have been proposed as alternatives to autografts, the success rate of these techniques remains poor, often resulting in immune rejection. Thus, researchers have invested considerable effort in developing synthetic nerve conduits for the repair of peripheral nerve defects.
Improvement in the renal prognosis in nephropathic cystinosis.

BACKGROUND AND OBJECTIVES Nephropathic cystinosis (NC) is an autosomal recessive disorder occurring in one to two per 100,000 newborns. Because of the rarity of NC, long-term outcome data are scarce. DESIGN, SETTING, PARTICIPANTS, & MEASUREMENTS 245 NC patients from 18 countries provided data to the ESPN/ERA-EDTA registry. We matched NC patients on renal replacement therapy (RRT) to non-NC children on RRT. RESULTS Between 1979 and 2008, mean age at the start of RRT among NC children increased by 0.15 year per calendar year (95% confidence interval, 0.10 to 0.21) from 8.8 to 12.7 years, whereas we did not observe this in non-NC children. Five-year survival after the start of RRT improved in NC patients from 86.1% (before 1990) to 100% (since 2000) as compared with the control population (89.6% and 94.0%). NC patients received a renal allograft more often (relative risk, 1.09; 95% confidence interval, 1.00 to 1.17) as compared with matched RRT children, and 5-year graft survival was better (94.0% versus 84.0%). NC dialysis patients were less often hypertensive than non-NC children matched for age, country, and dialysis modality (42.7% versus 51.7%) and had lower parathyroid hormone levels (median, 56 versus 140 pg/ml). Although height at start of RRT slightly improved during the past decade, children with NC remained significantly shorter than non-NC children at the start of RRT. CONCLUSIONS We demonstrated improved survival of the renal function as well as better patient and graft survival after the start of RRT in a large European cohort of NC patients over the last two decades.
Cabozantinib in the treatment of advanced renal cell carcinoma: clinical trial evidence and experience

The treatment of metastatic renal cell carcinoma (mRCC) is rapidly changing. During first-line treatment with targeted therapy, patients ultimately develop resistance to therapy and the disease progresses. Recently, cabozantinib has demonstrated a better response rate, progression-free survival and overall survival compared with everolimus after failure of prior targeted therapy in patients with advanced or metastatic renal cell carcinoma (RCC). Cabozantinib is a small-molecule tyrosine kinase inhibitor (TKI). It exerts inhibition of MET, vascular endothelial growth factor receptor type 2, AXL, and many other receptor tyrosine kinases that are also implicated in tumor pathobiology, including RET, KIT, and FLT3. MET drives tumor survival, invasion, angiogenesis, and metastasis through several downstream signaling pathways. AXL has recently been described as an essential mediator of cancer metastasis that mediates crosstalk and resistance to TKIs. MET and AXL are thought to be anti-vascular endothelial growth factor receptor (VEGF) resistance pathways and thus cabozantinib represents a logical choice after progression on initial VEGF therapy. Subgroup analyses examining those with good performance status or visceral and bone metastases indicate that the hazard ratios may be better when using cabozantinib versus everolimus. However, there were no clear statistically significant differences between any subgroups.
Enzyme I: the gateway to the bacterial phosphoenolpyruvate:sugar phosphotransferase system.

Regulatory aspects of the bacterial phosphoenolpyruvate (PEP):sugar phosphotransferase system (PTS) are reviewed. The structure and conformational stability of the first protein (enzyme I) of the PTS, as well as the requirement for enzyme I to dimerize for autophosphorylation by PEP in the presence of MgCl2 are discussed.
Dna content measurement can be obtained using archival material for dna flow cytometry a comparison with cytogenetic analysis in 56 pediatric solid tumors

Background. Although flow cytometry (FCM) has become a widely used technique for the measurement of DNA content in solid tumors, the correlation of ploidy analysis by FCM with cytogenetic analysis (CGA) is not well described. The sensitivities of G‐banded CGA and FCM were compared to determine the accuracy of the DNA index value (DI) as a measurement of chromosome number.