Miracle-dz/UniFAR-FTUs huggingface dataset:
On Interfacial Failure in Notched Unidirectional Glass/Epoxy Composites

The splitting mechanism in notched unidirectional glass/epoxy composites under tensile loading has been studied to gain insight into this failure process. An already- available mathematical expression based on the J-integral technique proposed by Tirosh [1] has been used for this purpose. This expression relates the length of the split crack to the in-plane elastic constants of the composite, original notch length, inter facial shear yield stress, and the applied tensile stress. This model has been used to distinguish between the quality of fiber-matrix bonding in two E-glass fiber-reinforced epoxy composites by evaluating their interfacial shear yield stress using transversely edge-notched unidirectional composites. The experimental results demonstrate that an important requirement to control the length of the split crack is higher fiber-matrix in terfacial shear yield stress. Also, the Tirosh model is found to effectively predict the progression of splitting in notched unidirectional composites.
Fourth‐order compact formulation of Navier–Stokes equations and driven cavity flow at high Reynolds numbers

A new fourth‐order compact formulation for the steady 2‐D incompressible Navier–Stokes equations is presented. The formulation is in the same form of the Navier–Stokes equations such that any numerical method that solve the Navier–Stokes equations can easily be applied to this fourth‐order compact formulation. In particular, in this work the formulation is solved with an efficient numerical method that requires the solution of tridiagonal systems using a fine grid mesh of 601 × 601. Using this formulation, the steady 2‐D incompressible flow in a driven cavity is solved up to Reynolds number with Re = 20 000 fourth‐order spatial accuracy. Detailed solutions are presented. Copyright © 2005 John Wiley & Sons, Ltd.
The Absence of Human Equilibrative Nucleoside Transporter 1 Is Associated with Reduced Survival in Patients With Gemcitabine-Treated Pancreas Adenocarcinoma

Purpose: Gemcitabine monotherapy is the standard palliative chemotherapy for pancreatic adenocarcinoma. Gemcitabine requires plasma membrane nucleoside transporter proteins to efficiently enter cells and exert it cytotoxicity. In vitro studies have demonstrated that deficiency of human equilibrative nucleoside transporter 1 (hENT1), the most widely abundant and distributed nucleoside transporter in human cells, confers resistance to gemcitabine toxicity, but the distribution and abundance of nucleoside transporters in normal and malignant pancreatic tissue is unknown. Experimental Design: We studied tumor blocks from normal pancreas and 21 Alberta patients with gemcitabine-treated pancreatic cancer. Immunohistochemistry on the formalin-fixed, paraffin-embedded tissues was performed with specific hENT1 and human Concentrative Nucleoside Transporter 3 monoclonal antibodies and scored by a pathologist blinded to clinical outcomes. Results: hENT1 was detected in normal Langerhan cells and lymphocytes but not in normal glandular elements. Patients in whom all adenocarcinoma cells had detectable hENT1 had significantly longer median survivals from gemcitabine initiation than those for whom hENT1 was absent in a proportion (10 to 100%) of adenocarcinoma cells (median survival, 13 versus 4 months, P = 0.01). Immunohistochemistry for human Concentrative Nucleoside Transporter 3 revealed moderate to high-intensity staining in all adenocarcinoma tissue samples. Conclusions: Patients with pancreatic adenocarcinoma with uniformly detectable hENT1 immunostaining have a significantly longer survival after gemcitabine chemotherapy than tumors without detectable hENT1. Immunohistochemistry for hENT1 shows promise as a molecular predictive assay to appropriately select patients for palliative gemcitabine chemotherapy but requires formal validation in prospective, randomized trials.
Identification of a Mutation in the Ileal Sodium-dependent Bile Acid Transporter Gene That Abolishes Transport Activity (*)

The ileal Na/bile acid cotransporter plays a critical role in the reabsorption of bile acids from the small intestine. In the course of cloning and characterizing the human ileal Na/bile acid cotransporter cDNA, a dysfunctional isoform was identified in a patient diagnosed with Crohn's disease. Expression studies using hamster-human ileal Na/bile acid cotransporter cDNA chimeras narrowed the location of the defect to the carboxyl-terminal 94 amino acids. Comparison of the sequence of the dysfunctional isoform to that of a wild-type human ileal Na/bile acid cotransporter genomic clone revealed a single C to T transition resulting in a proline to serine substitution at amino acid position 290. The inheritance of this mutation in the proband's family was confirmed by single-stranded conformation polymorphism analysis and DNA sequencing. In transfected COS-1 cells, the single amino acid change abolished taurocholate transport activity but did not alter the transporter's synthesis or subcellular distribution. This dysfunctional mutation represents the first known molecular defect in a human sodium-dependent bile acid transporter.
How and when does an anticancer drug leave its binding site?

We use atomistic simulations to elucidate the unbinding time scales and mechanisms of the cancer drug dasatinib from host kinase. Obtaining atomistic resolution of drug unbinding from a protein is a much sought-after experimental and computational challenge. We report the unbinding dynamics of the anticancer drug dasatinib from c-Src kinase in full atomistic resolution using enhanced sampling molecular dynamics simulations. We obtain multiple unbinding trajectories and determine a residence time in agreement with experiments. We observe coupled protein-water movement through multiple metastable intermediates. The water molecules form a hydrogen bond bridge, elongating a specific, evolutionarily preserved salt bridge and enabling conformation changes essential to ligand unbinding. This water insertion in the salt bridge acts as a molecular switch that controls unbinding. Our findings provide a mechanistic rationale for why it might be difficult to engineer drugs targeting certain specific c-Src kinase conformations to have longer residence times.
Caries risk profile using the Cariogram in governmental and private orthodontic patients at de-bonding.

OBJECTIVES To analyze various caries-related factors in orthodontic patients at de-bonding, and to test the null hypothesis that there is no difference in caries risk between governmental and private orthodontic patients immediately after orthodontic treatment. MATERIALS AND METHODS A cross-sectional examination was carried out on 89 orthodontic patients aged 13-29 years, mean age 21.5 years. They were divided into two groups based on the center of treatment, governmental group (G) (n = 45) and private group (P) (n = 44). The investigation comprised a questionnaire, plaque scoring, caries examination, bitewing radiographs, salivary secretion rate, buffering capacity, and cariogenic microorganisms. Data were entered into the Cariogram PC program to illustrate caries risk profiles. RESULTS Findings revealed that "the chance of avoiding new cavities," according to the Cariogram, was high in the P-group and low in the G-group (61% and 28%, respectively) (P < .001). Decayed, missing, and filled surfaces (DMFS), plaque index, mutans streptococcus and lactobacillus counts, and salivary buffer capacity were significantly higher in the G-group compared with the P-group (P < .05). The total number of caries lesions at de-bonding in the G-group was more than two times higher than that in the P-group (150 vs 68) (P < .001). CONCLUSIONS The "chance to avoid new cavities" in orthodontic patients at de-bonding was less in the governmental group compared with the private group, as illustrated by the Cariogram. The governmental group also had significantly less favorable values than the private group for most of the caries-related factors.
Types and Strains: Their Essential Role in Understanding Protein Aggregation in Neurodegenerative Diseases

Protein misfolding and aggregation is a key event in diseases like Alzheimer’s disease (AD) or Parkinson’s disease (PD) and is associated with neurodegeneration. Factors that initiate protein misfolding and the role of protein aggregation in the pathophysiology of disease pose major challenges to the neuroscientific community. Interestingly, although the accumulation of the same misfolded protein, e.g., α-synuclein is detectable in all idiopathic PD patients, the disease spectrum covers a variety of different clinical presentations and disease courses. In a more recent attempt this clinical variance is being explained in analogy to prion diseases by different protein aggregate conformations. In prion diseases a relationship between protein aggregate conformation properties and the clinical disease course was shown by relating different prion types to a dementia and an ataxic disease course in Creutzfeldt-Jakob patients. This principle is currently transferred to AD, PD and other neurodegenerative diseases with protein aggregation. However, differences in protein aggregate conformation are frequently addressed as disease strains. The term “strain” also derives from prion research and evolved by adopting the virus terminology at a time when transmissible spongiform encephalopathies (TSEs; later called prion diseases) were assumed to be caused by a virus. The problem is that in virus taxonomy the term “type” refers to properties of the disease agent itself and the term “strain” refers to host associated factors that interact with the disease agent and may moderately modify the clinical disease presentation. Strain factors can be discovered only after transmission and passaging of the agent in a host of a different species. The incorrect use of the terminology confuses disease agent and host factors and hampers the understanding of the pathophysiology of protein aggregate-associated neurodegenerative diseases. In this review article the discoveries are reviewed that explain how the terms “type” and “strain” emerged for unconventional disease agents. This may help to avoid confusion in the terminology of protein aggregation diseases and to reflect correctly the impact of protein aggregate conformation as well as host factor contribution on different clinical variations of AD, PD and other neurodegenerative diseases.
Unsupervised color image segmentation based on Gaussian mixture model

A novel color image segmentation method based on finite Gaussian mixture model is proposed in this paper. First, we use EM algorithm to estimate the distribution of input image data and the number of mixture components is automatically determined by MML criterion. Then the segmentation is carried out by clustering each pixel into appropriate component according to maximum likelihood (ML) criterion. The advantage of our method lies in its ability of less relying on initialization and segmenting images in a totally unsupervised manner. Experimental results show that our segmentation method can obtain better results than other methods.
BrkA Protein of Bordetella pertussisInhibits the Classical Pathway of Complement after C1 Deposition

ABSTRACT Bordetella pertussis produces a 73-kDa protein,BrkA (Bordetella resistance to killing), which inhibits the bactericidal activity of complement. In this study we characterized the step in the complement cascade where BrkA acts, using three strains: a wild-type strain, a strain containing an insertional disruption of brkA, and a strain containing two copies of the brkA locus. Following incubation with 10% human serum, killing was greatest for the BrkA mutant, followed by that for the wild-type strain, while the strain with two copies ofbrkA was the most resistant. Complement activation was monitored by enzyme-linked immunosorbent assay (ELISA) or Western blotting. ELISAs for SC5b-9, the soluble membrane attack complex, showed that production of SC5b-9 was greatest with thebrkA mutant, less with the wild type, and least with the strain containing two copies of brkA. Deposition of complement proteins on the bacteria was monitored by Western blotting. A decrease in deposition on the bacteria of C4, C3, and C9 corresponded with decreased complement sensitivity. Deposition of C1, however, was not affected by the presence of BrkA. These studies show that BrkA inhibits the classical pathway of complement activation and prevents accumulation of deposited C4.
Flexible and Tough Poly(lactic acid) Films for Packaging Applications: Property and Processability Improvement by Effective Reactive Blending

This study demonstrates a practical means to overcome inherent brittleness problem of poly(lactic acid) (PLA) and make PLA feasible as packaging material. PLA with suitable processability is utterly required for package manufacturers, where flexible, tough PLA film is essential for packers and end users. Highly flexible PLA films with 60‐fold increase in elongation at break (Eb) over that of the neat PLA were successfully produced by integrating effective reactive blending and economical film blowing process. The ‘two‐step’ blending was used to prepare PLA compound; poly(butylene adipate‐co‐terephthalate) (PBAT – another biodegradable polymer) was first blended with 0.5–1% chain extender (epoxy‐functionalized styrene acrylic copolymer) (ESA), followed by subsequent blending with PLA in twin‐screw extruder. Blown films of reactive blend of PLA/PBAT/ESA (80/20/1) showed impressively high Eb of 250% versus a very low Eb of 4% for the neat PLA. Resulting blown films still possessed high modulus of 2 GPa, yield stress of 50–60 MPa and good toughness of ~100 MPa. Significant enhancement in the film's ductility was attributed to homogeneous blend with developed fine strand‐like structure as a result of effective in situ compatibilization and good interfacial adhesion between the PLA and PBAT. PLA/PBAT/ESA blend also offered improved processability. Resulting films had acceptable haze of ~10% for common packaging, and clearer film close to PLA (≤2%) could be obtained by designing PLA skin layers in multilayer structure. Films of PLA/PBAT/1%ESA exhibit potential as packaging material; their mechanical and optical properties are comparable with or even exceed some existing films used in the market. Copyright © 2015 John Wiley & Sons, Ltd.
Dynamic geometry registration

We propose an algorithm that performs registration of large sets of unstructured point clouds of moving and deforming objects without computing correspondences. Given as input a set of frames with dense spatial and temporal sampling, such as the raw output of a fast scanner, our algorithm exploits the underlying temporal coherence in the data to directly compute the motion of the scanned object and bring all frames into a common coordinate system. In contrast with existing methods which usually perform pairwise alignments between consecutive frames, our algorithm computes a globally consistent motion spanning multiple frames. We add a time coordinate to all the input points based on the ordering of the respective frames and pose the problem of computing the motion of each frame as an estimation of certain kinematic properties of the resulting space-time surface. By performing this estimation for each frame as a whole we are able to compute rigid inter-frame motions, and by adapting our method to perform a local analysis of the space-time surface, we extend the basic algorithm to handle registration of deformable objects as well. We demonstrate the performance of our algorithm on a number of synthetic and scanned examples, each consisting of hundreds of scans.
MetalDetector v2.0: predicting the geometry of metal binding sites from protein sequence

MetalDetector identifies CYS and HIS involved in transition metal protein binding sites, starting from sequence alone. A major new feature of release 2.0 is the ability to predict which residues are jointly involved in the coordination of the same metal ion. The server is available at http://metaldetector.dsi. unifi.it/v2.0/.
Factors affecting the motivation of healthcare professionals providing care to Emiratis with type 2 diabetes

Objective We aimed to identify facilitators of and barriers to healthcare professionals' motivation in a diabetes centre in the United Arab Emirates (UAE). Design A qualitative research approach was employed using semistructured interviews to assess perception of and attitudes regarding healthcare professionals' motivation in providing good quality diabetes care. Setting A diabetes centre located in Abu-Dhabi, UAE. Participants Healthcare professionals including specialist physicians, dieticians, podiatrists, health educators and nurses were recruited through purposive sampling. Main outcome measures After data collection, the audiotaped interviews were transcribed verbatim and subjected to content analysis. Results Nine semistructured interviews were conducted with healthcare professionals of various professional backgrounds. Important facilitators and barriers related to patient, professional, organization and cultural factors were identified. Barriers that related to heavy workload, disjointed care, lack of patient compliance and awareness, and cultural beliefs and attitudes about diabetes were common. Key facilitators included the patient's role in achieving therapeutic outcomes as well as compliance, cooperation and communication. Conclusion This qualitative study provides some unique insights about factors affecting healthcare professionals' motivation in providing good quality care. To improve the motivation of healthcare professionals in the management of diabetes and therefore the quality of diabetes care, several steps are needed. Importantly, the role of primary care should be reinforced and strengthened regarding the management of type 2 diabetes mellitus, privacy of the consultation time should be highly protected and regulated, and awareness of the Emirate culture and its impact on health should be disseminated to the healthcare professionals providing care to Emirates with diabetes. Also, greater emphasis should be placed on educating Emiratis with diabetes on, and involving them in, the management of their condition.
Cell Response Strains Elicits a Distinct Effector T gingivalis Porphyromonas Cells by Minor Fimbriated Targeting of DC-SIGN on Human Dendritic

* The oral mucosal pathogen Porphyromonas gingivalis expresses at least two adhesins: the 67-kDa mfa-1 (minor) ﬁmbriae and the 41-kDa ﬁmA (major) ﬁmbriae. In periodontal disease, P. gingivalis associates in situ with dermal dendritic cells (DCs), many of which express DC-SIGN (DC-speciﬁc ICAM-3 grabbing nonintegrin; CD209). The cellular receptors present on DCs that are involved in the uptake of minor/major ﬁmbriated P. gingivalis , along with the effector immune response induced, are presently unclear. In this study, stably transfected human DC-SIGN (cid:1) / (cid:2) Raji cell lines and monocyte-derived DCs (MoDCs) were pulsed with whole, live, wild-type Pg381 or isogenic major (DPG-3)-, minor (MFI)-, or double ﬁmbriae (MFB)-deﬁcient mutant P. gingivalis strains. The inﬂuence of blocking Abs, carbohydrates, full-length glycosylated HIV-1 gp120 envelope protein, and cytochalasin D on the uptake of strains and on the immune responses was determined in vitro. We show that the binding of minor ﬁmbriated P. gingivalis strains to Raji cells and MoDCs is dependent on DC-SIGN, whereas the double ﬁmbriae mutant strain does not bind. Binding to DC-SIGN on MoDCs is followed by the internalization of P. gingivalis into DC-SIGN-rich intracellular compartments, and MoDCs secrete low levels of inﬂammatory cytokines and remain relatively immature. Blocking DC-SIGN with HIV-1 gp120 prevents the uptake of minor ﬁmbriated strains and deregulates the expression of inﬂammatory
The Potassium-Dependent Transcriptome of Arabidopsis Reveals a Prominent Role of Jasmonic Acid in Nutrient Signaling1[w]

Full genome microarrays were used to assess transcriptional responses of Arabidopsis seedlings to changing external supply of the essential macronutrient potassium (K+). Rank product statistics and iterative group analysis were employed to identify differentially regulated genes and statistically significant coregulated sets of functionally related genes. The most prominent response was found for genes linked to the phytohormone jasmonic acid (JA). Transcript levels for the JA biosynthetic enzymes lipoxygenase, allene oxide synthase, and allene oxide cyclase were strongly increased during K+ starvation and quickly decreased after K+ resupply. A large number of well-known JA responsive genes showed the same expression profile, including genes involved in storage of amino acids (VSP), glucosinolate production (CYP79), polyamine biosynthesis (ADC2), and defense (PDF1.2). Our findings highlight a novel role of JA in nutrient signaling and stress management through a variety of physiological processes such as nutrient storage, recycling, and reallocation. Other highly significant K+-responsive genes discovered in our study encoded cell wall proteins (e.g. extensins and arabinogalactans) and ion transporters (e.g. the high-affinity K+ transporter HAK5 and the nitrate transporter NRT2.1) as well as proteins with a putative role in Ca2+ signaling (e.g. calmodulins). On the basis of our results, we propose candidate genes involved in K+ perception and signaling as well as a network of molecular processes underlying plant adaptation to K+ deficiency.
Influence of temperature and concentration on the dynamic viscosity of sodium hypochlorite in comparison with 17% EDTA and 2% chlorhexidine gluconate: An in vitro study

Aims: The aim of this study was to assess the influence of temperature and concentration on the dynamic viscosity of sodium hypochlorite in comparison with 17% EDTA and 2% chlorhexidine gluconate. Settings and Design: In vitro Materials and Methods: Dynamic viscosity measurements of sodium hypochlorite [NaOCl (5.25%, 2.6%, 1.25%)], EDTA (17%), and chlorhexidine gluconate [CHX, 2%] were measured using a rotational digital viscometer at room temperature (25°C). The influence of temperature (45°C, 60°C) and concentration (5.25%, 2.6%, and 1.25%) on the dynamic viscosity of NaOCl was also evaluated. The measurements were performed using a circulating water bath calibrated with a thermostat, and the dynamic viscosity measurements were noted in Centipoise (Cps). Statistical Analysis Used: The tests used for the statistical analysis were Kolmogorov-Smirnov and Shapiro Wilk tests, one-way ANOVA, and independent sample t-test. Results: Viscosity statistically increased with NaOCl concentration and decreased with increasing temperature. Amongst the tested NaOCl groups, 5.25% NaOCl at room temperature was significantly the most viscous (μ =1.5300 Cps) while 1.25% NaOCl at 60°C was significantly the least viscous (μ =1.1800 Cps). Conclusions: 5.25% NaOCl and 17% EDTA are significantly viscous at room temperature. Elevating the temperature of 1.25% NaOCl to 60°C significantly reduces the viscosity of the NaOCl.