Miracle-dz/UniFAR-FTUs huggingface dataset:
A Linearized Crank-Nicolson-Galerkin Method for the Ginzburg-Landau Model

The time-dependent Ginzburg-Landau model is used extensively in studying the nonequilibrium state of superconductivity. The computer simulation of this model requires high-performance computing power and reliable and efficient numerical methods to solve the Ginzburg-Landau equtions. In this paper, a linearized Crank-Nicolson-Galerkin method is proposed for solving these nonlinear and coupled partial differential equations. The method uses the Galerkin finite element approximation in spatial discretization and the Crank-Nicolson implicit scheme in time discretization, together with certain techniques which linearize and decouple the Ginzburg-Landau equations. While retaining the stabillity and accuracy of the Crank-Nicolson scheme, the proposed approach results in symmetric and positive definite matrix problems, thus substantially improving the computational efficiency. Furthermore, and even more important, the proposed approach is suitable for large-scale parallel computation. Numerical results from simulating the vortex dynamics of superconductivity by using the linearized Crank-Nicolson-Galerkin method are presented.
Mobile phones: Reservoirs for the transmission of nosocomial pathogens

Background: Global burden of hospital-associated infection (HAI) is on the rise and contributes significantly to morbidity and mortality of the patients. Mobile phones are indispensible part of communication among doctors and other health care workers (HCWs) in hospitals. Hands of HCWs play an important role in transmission of HAI and mobile phones which are seldom cleaned and often touched during or after the examination of patients without hand washing can act as a reservoir for transmission of potent pathogens. This study aimed to investigate the rate of bacterial contamination of mobile phones among HCWs in our tertiary care hospital and to compare it with personal mobile phones of non-HCWs (control group). Materials and Methods: The mobile phones and dominant hands of 386 participants were sampled from four different groups, hospital doctors and staff (132), college faculty and staff (54), medical students (100) and control group (100). Informed consent and questionnaire was duly signed by all the participants. Samples were processed according to standard guidelines. Results: 316 mobile phones (81.8%) and 309 hand swab samples (80%) showed growth of bacterial pathogens. The most predominant isolates were Coagulase-negative Staphylococcus, Staphylococcus aureus, Acinetobacter species, Escherichia coli, Klebsiella pneumoniae, Pseudomonas species and Enterococcus species. Conclusion: Hundred percent contamination was found in mobile phones and hands of HCWs indicating mobile phones can be the potential source of nosocomial pathogens. Our study results suggest that use of mobile phones in health care setup should be restricted only for emergency calls. Strict adherence to infection control policies such as proper hand hygiene practices should be followed.
Subtle Deficits in Instrumental Activities of Daily Living in Subtypes of Mild Cognitive Impairment

Background/Aims: Greater cognitive and functional deficits in mild cognitive impairment (MCI) are associated with higher rates of dementia. We explored the relationship between these factors by comparing instrumental activities of daily living (IADLs) among cognitive subtypes of MCI and examining associations between IADL and neuropsychological indices. Methods: We analyzed data from 1,108 MCI and 3,036 normal control subjects included in the National Alzheimer’s Coordinating Center Uniform Data Set who were assessed with the Functional Activities Questionnaire (FAQ). Results: IADL deficits were greater in amnestic than nonamnestic MCI, but within these subgroups, did not differ between those with single or multiple domains of cognitive impairment. FAQ indices correlated significantly with memory and processing speed/executive function. Conclusions: IADL deficits are present in both amnestic MCI and nonamnestic MCI but are not related to the number of impaired cognitive domains. These cross-sectional findings support previous longitudinal reports suggesting that cognitive and functional impairments in MCI may be independently associated with dementia risk.
Biophysical Characterization of Lipopolysaccharide and Lipid A Inactivation by Lactoferrin

Abstract The interaction of bacterial endotoxins (LPS Re and lipid A, the endotoxic principle of LPS) with the endogenous antibiotic lactoferrin (LF) was investigated using various physical techniques and biological assays. By applying Fouriertransform infrared (FTIR) spectroscopy, we find that LF binds to the phosphate group within the lipid A part and induces a rigidification of the acyl chains of LPS. The secondary structure of the protein as monitored by the amide I band is, however, not changed. Concomitant with the IR data, scanning calorimetric data indicate a sharpening of the acyl chain phase transition. From titration calorimetric and zeta potential data, saturation of LF binding to LPS was found to lie at a : ratio of 1:3 to 1:5 M from the former and 1:10 M from the latter technique. Xray scattering data indicate a change of the lipid A aggregate structure from inverted cubic to multilamellar, and with fluorescence (FRET) spectroscopy, LF is shown to intercalate by itself into phospholipid liposomes and may also block the lipopolysaccharidebinding protein (LBP)induced intercalation of LPS. The LPSinduced cytokine production of human mononuclear cells exhibits a decrease due to LF binding, whereas the coagulation of amebocyte lysate in the Limulus test exhibited concentrationdependent changes. Based on these results, a model for the mechanisms of endotoxin inactivation by LF is proposed.
Organization and expression of genetic determinants for synthesis and assembly of type 51 R bodies

Type 51 R bodies are produced by all bacterial endosymbionts (Caedibacter taeniospiralis) of Paramecium tetraurelia that confer the hump-killer trait upon their hosts. Type 51 R-body synthesis by C. taeniospiralis is required for expression of the hump-killer trait. The genetic determinants for type 51 R-body synthesis by C. taeniospiralis 47 have been cloned and expressed in Escherichia coli. In this communication we describe three species of polypeptides required for R-body synthesis and the organization of their genetic determinants. Each polypeptide species is controlled by a separate gene that is expressed as an independent transcriptional unit possessing regulatory signals that are recognized by E. coli. Two polypeptide species of 10 and 18 kilodaltons are required for R-body synthesis but apparently are not structural subunits. The third polypeptide species (13 kilodaltons) is the major structural subunit. R-body assembly involves polymerization reactions that result in high-molecular-mass polypeptide complexes, primarily composed of the 13-kilodalton polypeptide species, that appear to be the result of covalent cross-linking between structural subunits. The results presented here have been suggested to apply to the assembly and structure of all type 51 R bodies, but not necessarily to other R-body types.
Comparison of colour spaces for optic disc localisation in retinal images

The location of the optic disc is of critical importance in retinal image analysis. In this work we improve on an approach introduced by Mendels, Heneghan and Thiran (1999) which localises an optic disc region through grey level morphology, followed by snake fitting. We propose and implement both the automatic initialisation of the snake and the application of morphology in colour space. We examine various methods of performing the morphology step (to remove the interference of blood vessels) and compare them against each other. We demonstrate that our proposed simple Lab colour morphology method is particularly suitable for the characteristics of our optic disc images. Results indicate 90.32% average accuracy in localising, the optic disc boundary.
Case Control Analyses of Acute Endophthalmitis after Cataract Surgery in South India Associated with Technique, Patient Care, and Socioeconomic Status

Purpose. We investigated acute endophthalmitis incidence following cataract surgery vis-a-vis the current technological and postoperative care changes in higher and lower socioeconomic categories of patients in South India. Methods. In a retrospective case control study, we analyzed 62 cases of acute endophthalmitis and 5 controls for each endophthalmitis case from 46,095 cataract surgeries done between years 1993 and 1998. The time period covered the transition of surgical technique and after care. In addition, we analyzed systemic diseases, surgeon factor, habitat, and socioeconomic status. Results. Clinical and culture positive endophthalmitis incidence were 0.13% and 0.07%, respectively. Differential incidence of 0.10% and 0.17% for in- and ambulatory care surgeries, respectively, was close to statistical significance (P = 0.054). Lower economy category ambulatory patients had higher risk of infection. Conclusion. Ambulatory cataract surgery carried additional risk for post-operative infection in lower socioeconomic group. Improved health education could ensure greater safety.
O-linked β-N-acetylglucosamine modification of proteins is activated in post-ischemic brains of young but not aged mice: Implications for impaired functional recovery from ischemic stress

To evaluate the effect of age on the response of brains to an ischemic challenge, we subjected young and aged mice to transient forebrain ischemia, and analyzed the heat shock response and unfolded protein response, ubiquitin conjugation and SUMO conjugation, and O-linked β-N-acetylglucosamine modification of proteins (O-GlcNAcylation). The most prominent age-related difference was an inability of aged mice to activate O-GlcNAcylation. Considering many reports on the protective role of O-GlcNAcylation in various stress conditions including myocardial ischemia, this pathway could be a promising target for therapeutic intervention to improve functional recovery of aged patients following brain ischemia.
Inhibition of Cytochrome P450 (CYP3A4) Activity by Extracts from 57 Plants Used in Traditional Chinese Medicine (TCM)

Background: Herbal medicine is widely used all over the world for treating various health disorders. It is employed either alone or in combination with synthetic drugs or plants to be more effective. Objective: The assessment of the effect of both water and methanol extracts of 57 widely used plants from Traditional Chinese Medicine (TCM) against the main phase I metabolizing enzyme CYP3A4 in vitro for the first time. Materials and Methods: The inhibition of cytochrome P450 activity was evaluated using a luminescence assay. The principal component analysis (PCA) was used to correlate the inhibitory activity with the main secondary metabolites present in the plant extracts. Molecular modeling studies on CYP3A4 (PDB ID 4NY4) were carried out with 38 major compounds present in the most active plant extracts to validate the observed inhibitory effect. Results: Aqueous extracts of Acacia catechu, Andrographis paniculata, Arctium lappa, Areca catechu, Bupleurum marginatum, Chrysanthemum indicum, Dysosma versipellis, and Spatholobus suberectus inhibited CYP3A4 is more than 85% (at a dose of 100 μg/mL). The corresponding methanol extracts of A. catechu, A. paniculata, A. catechu, Mahonia bealei, and Sanguisorba officinalis inhibited the enzyme by more than 50%. Molecular modeling studies revealed that two polyphenols, namely hesperidin and rutin, revealed the highest fitting scores in the active sites of the CYP3A4 with binding energies equal to -74.09 and -71.34 kcal/mol, respectively. Conclusion: These results provide evidence that many TCM plants can inhibit CYP3A4, which might cause a potential interference with the metabolism of other concomitantly administered herbs or drugs. Abbreviation used: CHARMm: Chemistry at HARvard Macromolecular Mechanics, CYP: Cytochrome P450, DMSO: Dimethyl Sulfoxide, PCA: Principal Component Analysis, PDB: Protein Data Bank, TCM: Traditional Chinese Medicine
Circulating microRNA (miRNA) Expression Profiling in Plasma of Patients with Gestational Diabetes Mellitus Reveals Upregulation of miRNA miR-330-3p

Gestational diabetes mellitus (GDM) is characterized by insulin resistance accompanied by low/absent beta-cell compensatory adaptation to the increased insulin demand. Although the molecular mechanisms and factors acting on beta-cell compensatory response during pregnancy have been partially elucidated and reported, those inducing an impaired beta-cell compensation and function, thus evolving in GDM, have yet to be fully addressed. MicroRNAs (miRNAs) are a class of small endogenous non-coding RNAs, which negatively modulate gene expression through their sequence-specific binding to 3′UTR of mRNA target. They have been described as potent modulators of cell survival and proliferation and, furthermore, as orchestrating molecules of beta-cell compensatory response and function in diabetes. Moreover, it has been reported that miRNAs can be actively secreted by cells and found in many biological fluids (e.g., serum/plasma), thus representing both optimal candidate disease biomarkers and mediators of tissues crosstalk(s). Here, we analyzed the expression profiles of circulating miRNAs in plasma samples obtained from n = 21 GDM patients and from n = 10 non-diabetic control pregnant women (24–33 weeks of gestation) using TaqMan array microfluidics cards followed by RT-real-time PCR single assay validation. The results highlighted the upregulation of miR-330-3p in plasma of GDM vs non-diabetics. Furthermore, the analysis of miR-330-3p expression levels revealed a bimodally distributed GDM patients group characterized by high or low circulating miR-330 expression and identified as GDM-miR-330high and GDM-miR-330low. Interestingly, GDM-miR-330high subgroup retained lower levels of insulinemia, inversely correlated to miR-330-3p expression levels, and a significant higher rate of primary cesarean sections. Finally, miR-330-3p target genes analysis revealed major modulators of beta-cell proliferation and of insulin secretion, such as the experimentally validated genes E2F1 and CDC42 as well as AGT2R2, a gene involved in the differentiation of mature beta-cells. In conclusion, we demonstrated that plasma miR-330-3p could be of help in identifying GDM patients with potential worse gestational diabetes outcome; in GDM, miR-330-3p may directly be transferred from plasma to beta-cells thus modulating key target genes involved in proliferation, differentiation, and insulin secretion.
Prevalence of Human Papillomavirus Genotypes in Cervical Cancer

Background and Objective Cervical cancer is the second most common female genital cancer worldwide. There is strong epidemiological and molecular evidence indicating that human papillomavirus (HPV) infection is a necessary event in the development of cervical intraepithelial lesion and subsequent invasive carcinoma. The aim of this study was to investigate the HPV genotype distribution and prevalence in cervical cancer of Thai women. Materials and Methods One hundred fifty-five cervical cancer specimens were enrolled in this study. The HPV genotypes were determined by means of the combined use of a line probe assay (INNO-LiPA) and DNA chip methods. Results Of the overall prevalence of HPV in the study group, 83.2% and 11.6% of the cases had single and multiple genotype infections, respectively. The most prevalent genotypes were HPV 16 (51%), followed by HPV 18 (20%), HPV 52 (10.3%), HPV 58 (5.8%), and HPV 33 (4.5%). All HPV genotypes found in this study could be classified as 13 high-risk HPV, 2 low-risk HPV, and 2 additional types. Of the specimens, 94.8% had at least one high-risk HPV genotype infection. Conclusion As for the potential benefits of commercially available prophylactic vaccines to prevent HPV infection in Thailand, both vaccines (bivalent and quadrivalent) can protect from HPV-related cervical cancer in only approximately 71%. Therefore, screening programs such as routine Papanicolaou test, cytology, and HPV DNA detection are still essential for cervical cancer prevention. Moreover, future generations of HPV vaccines should also include the other most common genotypes and decrease the severe adverse effects reported at the present time.
Exploring the Uncanny Valley with Japanese Video Game Characters

Dr. Masahiro Mori’s robotics design theory, the Uncanny Valley, has become a common reference in virtual character design. The theory holds that robots whose appearance is very close to being human, but not fully, will evoke a very negative human reaction. The theory is often referenced in design outside of robots, especially in video games, but there is very little data to support this application. The attempts at photorealistic graphics in the latest round of video game hardware have made reference to the valley common in even mass media discussion. This study asked 60 subjects their opinions on 75 different virtual characters from both inside and outside video games to investigate the relationship between human-like appearance and attraction. The results found definite parallels between Mori’s predictions with robots and subject opinion on virtual characters, and have direct application to video game character design.
Human phosphatase CDC14A is recruited to the cell leading edge to regulate cell migration and adhesion

Significance Cell migration and adhesion play critical roles in animal development and tumor metastasis and are regulated by protein phosphorylation. Here we identified the human phosphatase hCDC14A (human cell-division cycle 14A) as F-actin binding protein at the leading edge that regulates both processes. Loss of hCDC14A activity promotes cell mobility and reduces cell adhesion. Importantly, cells devoid of hCDC14A activity were more invasive in a colony-forming assay. Database analysis indicates that hCDC14A expression is frequently down-regulated in cancer tissues and is associated with poor patient prognosis. Thus, the promigratory impact of hCDC14A inactivation upon the F-actin cytoskeleton supports tumor proliferation and metastasis. This hCDC14A function is clearly distinct from the mitotic functions of the budding and fission yeast orthologs Cdc14/Flp1. Cell adhesion and migration are highly dynamic biological processes that play important roles in organ development and cancer metastasis. Their tight regulation by small GTPases and protein phosphorylation make interrogation of these key processes of great importance. We now show that the conserved dual-specificity phosphatase human cell-division cycle 14A (hCDC14A) associates with the actin cytoskeleton of human cells. To understand hCDC14A function at this location, we manipulated native loci to ablate hCDC14A phosphatase activity (hCDC14APD) in untransformed hTERT-RPE1 and colorectal cancer (HCT116) cell lines and expressed the phosphatase in HeLa FRT T-Rex cells. Ectopic expression of hCDC14A induced stress fiber formation, whereas stress fibers were diminished in hCDC14APD cells. hCDC14APD cells displayed faster cell migration and less adhesion than wild-type controls. hCDC14A colocalized with the hCDC14A substrate kidney- and brain-expressed protein (KIBRA) at the cell leading edge and overexpression of KIBRA was able to reverse the phenotypes of hCDC14APD cells. Finally, we show that ablation of hCDC14A activity increased the aggressive nature of cells in an in vitro tumor formation assay. Consistently, hCDC14A is down-regulated in many tumor tissues and reduced hCDC14A expression is correlated with poorer survival of patients with cancer, to suggest that hCDC14A may directly contribute to the metastatic potential of tumors. Thus, we have uncovered an unanticipated role for hCDC14A in cell migration and adhesion that is clearly distinct from the mitotic and cytokinesis functions of Cdc14/Flp1 in budding and fission yeast.
Preemptive routing in Ad Hoc networks

Existing on-demand ad-hoc routing algorithms initiate route discovery only after a path breaks, incurring a significant cost in detecting the disconnection and establishing a new route. In this work, we investigate adding proactive route selection and maintenance to on-demand ad-hoc routing algorithms. More specifically, when a path is likely to be broken, a warning is sent to the source indicating the likelihood of a disconnection. The source can then initiate path discovery early, potentially avoiding the disconnection altogether. A path is considered likely to break when the received packet power becomes close to the minimum detectable power (other approaches are possible). Care must be taken to avoid initiating false route warnings due to fluctuations in received power caused by fading, multipath effects and similar random transient phenomena. Experiments demonstrate that adding proactive route selection and maintenance to DSR and AODV (on-demand ad hoc routing protocols) significantly reduces the number of broken paths, with a small increase in protocol overhead. Packet latency and jitter also goes down in most cases. We also show some experimental results obtained by running TCP on top of the proactive routing schemes proposed. Several improvements and extensions are also discussed. Pro-active route selection and maintenance is general and can be used with other routing algorithms and optimizations to them.
Oxford Handbook of Psychiatry

Covering all major psychiatric conditions and sub-specialties, this handbook provides practical and comprehensive guidelines and in-depth coverage of psychiatric assessment, psychopathology, evidence-based practice, therapeutic issues, and transcultural psychiatry. Fully up-to-date with the latest revisions of the DSM-IV and the ICD10, it is indexed alphabetically by classification codes and acute presentations for quick access. It reflects the recent major changes to psychiatric training and examination as well as the latest drug information. Reviewed by experienced clinicians, and revised by Specialist Trainees, this handbook not only gives expert advice for psychiatry professionals, but is also directly relevant to trainees in psychiatry. For the third edition, new information includes guidance on Adult ADHD, information on new drugs of abuse (e,g, GBL, GHB, mephodrone), and clinical decision-making in the prison setting. With such broad coverage and depth of guidance, this is the must-have pocket guide for all professionals and trainees working in psychiatry.
Reputation with Analogical Reasoning 1 Introduction 1 . 1 Reputations

We consider a repeated interaction between a long-run player and a sequence of short-run players, in which the long-run player may either be rational or may be a mechanical type who plays the same (possibly mixed) action in every stage game. We depart from the classic model, exemplified by Fudenberg and Levine [4, 5], in assuming that the short-run players make inferences by analogical reasoning, meaning that they correctly identify the average strategy of each type of long-run player, but do not recognize how this play varies across histories. Concentrating on 2 × 2 games, we provide a complete characterization of equilibrium payoffs, establishing a payoff bound for the rational long-run player that can be strictly larger than the familiar “Stackelberg” bound. We also provide a complete characterization of equilibrium behavior, showing that play begins with either a reputation-building or (depending on parameters) a reputation-spending stage, followed by a reputation-manipulation stage. ∗We thank Olivier Compte, Drew Fudenberg, Rani Spiegler, and Asher Wolinsky for helpful discussions. Jehiel thanks the European Research Council for financial support. Samuelson thanks the National Science Foundation (SES-0850263) for financial support. Reputation with Analogical Reasoning