Miracle-dz/UniFAR-FTUs huggingface dataset:
Uterine adenomyosis and infertility, review of reproductive outcome after in vitro fertilization and surgery

This review includes an analysis of the clinical studies evaluating reproductive outcome and adenomyosis, and a review of studies on reproductive outcome and surgical treatment options for adenomyosis. Strict diagnostic criteria and classification of disease are needed for an image diagnosis of adenomyosis. Studies of in vitro fertilization/intracytoplasmic sperm injection (IVF/ICSI) populations and women with surgically treated deep endometriosis have suggested that adenomyosis has a negative impact on reproductive outcome, although there are substantial variations between studies. Few data are available on the relation between the extent of disease and impact on reproductive outcome, but a correlation appears to exist. Case series seem to confirm a positive effect of gonadotropin‐releasing hormone analog treatment and surgery on reproductive outcome, but there are no controlled trials. Evidence is impaired by the poor quality of many studies, a lack of strict image diagnosis, and the absence of a classification of the extent of disease. Selection of the optimal evidence‐based treatment options for adenomyosis in the fertility clinic is difficult because of a lack of evidence regarding the relation between fertility and the degree and composition of adenomyosis. Adenomyosis may reduce implantation so severely that surgical or other treatment options should be recommended, but the benefit of these treatment options needs to be verified. Referral of women with adenomyosis and recurrent miscarriage and repeated failure of assisted reproductive technology to centers with a special interest in adenomyosis research and treatment may be critical.
450 ome of the white rot fungus Phanerochaete chrysosporium : structure , evolution and regulation of expression of genomic P 450 clusters

The model white rot fungus Phanerochaete chrysosporium has the extraordinary ability to degrade (to CO2) lignin and detoxify a variety of chemical pollutants. Whole genome sequencing of this fungus has revealed the presence of the largest P450ome in fungi comprising approx. 150 P450 genes, most of which have unknown function. On the basis of our genome-wide structural and evolutionary analysis, these P450 genes could be classified into 12 families and 23 subfamilies and under 11 fungal P450 clans. The analysis further revealed an extensive gene clustering with a total of 16 P450 clusters constituted of up to 11 members per cluster. In particular, evidence and role of gene duplications and horizontal gene transfer in the evolution of these P450 clusters have been discussed using two of the P450 families [CYP63 and CYP505 (where CYP is cytochrome P450)] as examples. In addition, the observed differential transcriptional induction of the clustered members of the CYP63 gene family, in response to different xenobiotic chemicals and carbon sources, indicated functional divergence within the P450 clusters, of this basidiomycete fungus. Introduction The basidiomycetous white rot fungus Phanerochaete chrysosporium, originally known to degrade lignin and other plant cell-wall components as a part of the Nature’s carbon cycle, has been shown to possess an extraordinary ability to oxidize and detoxify a broad range of toxic chemical pollutants. Initially, ligninolytic peroxidases were thought to be primarily involved in the lignin and xenobiotic oxidation processes under secondary metabolic (nutrient-limited) conditions. However, subsequent lines of evidence based on oxidizability of xenobiotic chemicals in the absence of peroxidase expression [1–4] as well as recent sequencing of the P. chrysosporium genome have led to the increased interest in alternate oxygenases particularly P450 mono-oxygenases, in this versatile xenobiotic biodegrader and detoxifier. Cytochrome P450 mono-oxygenases (‘P450s’) are a superfamily of haem-thiolate proteins that are involved in the metabolism of a wide variety of endogenous and xenobiotic compounds. P450 enzymes are found in different life forms including prokaryotes (archaea and bacteria), lower eukaryotes (fungi and insects) and higher eukaryotes (plants and animals including humans). A typical eukaryotic P450 system primarily consists of a P450 mono-oxygenase and a POR (NADPH:P450 oxidoreductase), both associated with membranes in the endoplasmic reticulum. However, soluble
Estimation of the detectability of optical orphan afterglows

Aims. By neglecting sideways expansion of gamma-ray burst (GRB) jets and assuming their half-opening angle distribution, we estimate the detectability of orphan optical afterglows. Methods. This estimation is carried out by calculating the durations of off-axis optical afterglows whose flux density exceeds a certain observational limit. Results. We show that the former assumption leads to more detectable orphans, while the latter suppresses the detectability strongly compared with the model with half-opening angle $\theta_{\rm j}=0.1$. We also considered the effects of other parameters, and find that the effects of the ejecta energy E j and post-jet-break temporal index $-\alpha_2$ are important but that the effects of the electron-energy distribution index p , electron energy equipartition factor $\epsilon_{\rm e}$, and environment density n are insignificant. If E j and $\alpha_2$ are determined by other methods, one can constrain the half-opening angle distribution of jets by observing orphan afterglows. Adopting a set of “standard” parameters, the detectable rate of orphan afterglows is about 1.3 $\times$ $10^{-2}~{\rm deg}^{-2}~{\rm yr}^{-1}$, if the observed limiting magnitude is 20 in R -band.
The treatment of common mental health problems in general practice.

BACKGROUND Previous studies report GPs under-treat mental health disorders, particularly depression, and treatments are non-specific and lack an evidence base. They conclude further training and education of GP's is required. OBJECTIVE To describe the treatment of common mental health disorders in relation to the level and severity of psychological problems as defined by the GP and external assessment. METHODS Cross sectional survey of General Practice attenders in New Zealand. Fifty consecutive adult patients were recruited from each practice of 70 randomly selected GP's. The psychological status of 773 respondents selected via the General Health Questionnaire (GHQ) was assessed, and details of management provided. Management options were compared with the level of psychological problem identified by the GP. RESULTS Treatment varied depending on the level of problem identification, and frequency of consultation, from 93% given treatment when an explicit diagnosis was made to 22.3% in patients with subclinical symptoms. The most commonly given treatment with an explicit diagnosis was psychotropic medication [73% (95% CI 63.6-82.9)] while for those patients with subclinical symptoms the most common form of treatment was discussion and counselling [15.7% (7.1-24.2)]. Only 1.7% (0.3-3.0) of patients with subclinical symptoms received psychotropics. CONCLUSION There is a clear association between the level of psychological problem identified and treatment. In contrast to previous views that treatment often appears to be given regardless of diagnosis, these results provide a picture of general practice management of common mental disorders more in line with evidence-based practice than previously described.
CAN RESIDENTIAL WIRELESS LANS PLAY A ROLE IN 4 G ?

We present a P2P scheme that could fuel the deployment of free public wireless LANs (WLANs) in cities; these WLANs would complement existing and future cellular networks. We call our scheme the P2P Wireless Network Confederation (P2PWNC). Unlike existing approaches, P2PWNC does not rely on central planning or altruistic groups. In P2PWNC, wireless service is provided to those who provide service to others based on an algorithm that detects non simultaneous exchanges, which runs in isolation on every peer. This indirect reciprocity algorithm resists the Sybil attack and promotes cooperation without relying on trusted authorities, persistent identities, or tamperproof modules. In this paper, we present P2PWNC as another component of the emerging 4G landscape.
Weekend Delay in Initiation of Chemotherapy for Acute Lymphoblastic Leukemia: Does it Matter?

The Friday afternoon admission of a child with a potential diagnosis of leukemia creates perceived delays in treatment initiation. Although generally not felt to affect prognosis, the effect of a few days delay in chemotherapy for children with acute lymphoblastic leukemia (ALL) has not been fully investigated. We retrospectively analyzed 207 patients consecutively diagnosed with ALL at Children’s Hospital & Research Center Oakland from 1995 to 2007 to determine if delay in chemotherapy increased the risk of relapse, death, transfer to the intensive care unit, or bacteremia. Friday admission did not significantly delay chemotherapy initiation with treatment started at a mean of 4.13±2.40 days for Friday admits versus 3.72±1.57 days for all others (P=0.29). There was no significant association between treatment delay days and relapse (P=0.94) or death (P=0.55). In Cox regression analysis, treatment delay was not a predictor of time to relapse (P=0.80) or longer duration of hospitalization (corrected for delay, P=0.15). There were trends toward significant associations between treatment delay and bacteremia (P=0.07) and intensive care unit admissions (P=0.08), although both were associated with shorter, not longer, treatment delays. We were unable to demonstrate a significant effect of delay in chemotherapy initiation for pediatric patients with newly diagnosed ALL on the examined outcome variables.
IITB System for CoNLL 2013 Shared Task: A Hybrid Approach to Grammatical Error Correction

We describe our grammar correction system for the CoNLL-2013 shared task. Our system corrects three of the five error types specified for the shared task noun-number, determiner and subject-verb agreement errors. For noun-number and determiner correction, we apply a classification approach using rich lexical and syntactic features. For subject-verb agreement correction, we propose a new rulebased system which utilizes dependency parse information and a set of conditional rules to ensure agreement of the verb group with its subject. Our system obtained an F-score of 11.03 on the official test set using the M 2 evaluation method (the official evaluation method).
Candida albicans cell surface superoxide dismutases degrade host-derived reactive oxygen species to escape innate immune surveillance

Mammalian innate immune cells produce reactive oxygen species (ROS) in the oxidative burst reaction to destroy invading microbial pathogens. Using quantitative real‐time ROS assays, we show here that both yeast and filamentous forms of the opportunistic human fungal pathogen Candida albicans trigger ROS production in primary innate immune cells such as macrophages and dendritic cells. Through a reverse genetic approach, we demonstrate that coculture of macrophages or myeloid dendritic cells with C. albicans cells lacking the superoxide dismutase (SOD) Sod5 leads to massive extracellular ROS accumulation in vitro. ROS accumulation was further increased in coculture with fungal cells devoid of both Sod4 and Sod5. Survival experiments show that C. albicans mutants lacking Sod5 and Sod4 exhibit a severe loss of viability in the presence of macrophages in vitro. The reduced viability of sod5Δ/Δ and sod4Δ/Δsod5Δ/Δ mutants relative to wild type is not evident with macrophages from gp91phox−/− mice defective in the oxidative burst activity, demonstrating a ROS‐dependent killing activity of macrophages targeting fungal pathogens. These data show a physiological role for cell surface SODs in detoxifying ROS, and suggest a mechanism whereby C. albicans, and perhaps many other microbial pathogens, can evade host immune surveillance in vivo.
Calling Biomarkers in Milk Using a Protein Microarray on Your Smartphone

Here we present the concept of a protein microarray-based fluorescence immunoassay for multiple biomarker detection in milk extracts by an ordinary smartphone. A multiplex immunoassay was designed on a microarray chip, having built-in positive and negative quality controls. After the immunoassay procedure, the 48 microspots were labelled with Quantum Dots (QD) depending on the protein biomarker levels in the sample. QD-fluorescence was subsequently detected by the smartphone camera under UV light excitation from LEDs embedded in a simple 3D-printed opto-mechanical smartphone attachment. The somewhat aberrant images obtained under such conditions, were corrected by newly developed Android-based software on the same smartphone, and protein biomarker profiles were calculated. The indirect detection of recombinant bovine somatotropin (rbST) in milk extracts based on altered biomarker profile of anti-rbST antibodies was selected as a real-life challenge. RbST-treated and untreated cows clearly showed reproducible treatment-dependent biomarker profiles in milk, in excellent agreement with results from a flow cytometer reference method. In a pilot experiment, anti-rbST antibody detection was multiplexed with the detection of another rbST-dependent biomarker, insulin-like growth factor 1 (IGF-1). Milk extract IGF-1 levels were found to be increased after rbST treatment and correlated with the results obtained from the reference method. These data clearly demonstrate the potential of the portable protein microarray concept towards simultaneous detection of multiple biomarkers. We envisage broad application of this ‘protein microarray on a smartphone’-concept for on-site testing, e.g., in food safety, environment and health monitoring.
Wnt5a cooperates with canonical Wnts to generate midbrain dopaminergic neurons in vivo and in stem cells

Wnts are a family of secreted proteins that regulate multiple steps of neural development and stem cell differentiation. Two of them, Wnt1 and Wnt5a, activate distinct branches of Wnt signaling and individually regulate different aspects of midbrain dopaminergic (DA) neuron development. However, several of their functions and interactions remain to be elucidated. Here, we report that loss of Wnt1 results in loss of Lmx1a and Ngn2 expression, as well as agenesis of DA neurons in the midbrain floor plate. Remarkably, a few ectopic DA neurons still emerge in the basal plate of Wnt1−/− mice, where Lmx1a is ectopically expressed. These results indicate that Wnt1 orchestrates DA specification and neurogenesis in vivo. Analysis of Wnt1−/−;Wnt5a−/− mice revealed a greater loss of Nurr1+ cells and DA neurons than in single mutants, indicating that Wnt1 and Wnt5a interact genetically and cooperate to promote midbrain DA neuron development in vivo. Our results unravel a functional interaction between Wnt1 and Wnt5a resulting in enhanced DA neurogenesis. Taking advantage of these findings, we have developed an application of Wnts to improve the generation of midbrain DA neurons from neural and embryonic stem cells. We thus show that coordinated Wnt actions promote DA neuron development in vivo and in stem cells and suggest that coordinated Wnt administration can be used to improve DA differentiation of stem cells and the development of stem cell-based therapies for Parkinson’s disease.
Patient recall of medication details in the outpatient clinic. Audit and assessment of the value of printed instructions requesting patients to bring medications to clinic

Objective: There is no ambiguity when a patient presents their medications in the correct packaging during a consultation and declares, “this is what I am taking, doctor, I take this many, at this time”. The aim of this study was to establish the prevalence of consultations in which patients attend both “empty handed” and unsure of their treatment. A re-evaluation was made after a simple intervention. Design: Prospective cross sectional study with subsequent intervention and re-evaluation based on patient completed questionnaire. Setting: University hospital cardiology outpatient department. Patients: Consecutive patients arriving at clinic reception desks. Results: Altogether 774 of 857 patients were receiving treatment; 15% attended with their tablets and 28% provided a note of their medication in some form; 40% attended empty handed but confident they could recall all aspects of their treatment from memory; 17% attended empty handed and unsure of their treatment. Intervention: Clinic appointment cards were stamped with the request PLEASE BRING YOUR MEDICATIONS WITH YOU TO THE CARDIOLOGY CLINIC. A second unrelated cohort of patients was then surveyed in an identical manner, nine months later. Of these, 329 of 376 patients were receiving medication. Those attending with their tablets in hand now accounted for 78% rather than 15% (χ2=423, df=2, p<0.001). The group unsure of their treatment, but attending empty handed, fell from 17% to 2%. Conclusions: Reprinted appointment cards are highly successful in encouraging patients to attend with their tablets. This provides reliable information for decision making.
MLS-based scalar fields over triangle meshes and their application in mesh processing

A novel technique that uses the Moving Least Squares (MLS) method to interpolate sparse constraints over mesh surfaces is introduced in this paper. Given a set of constraints, the proposed technique constructs, directly on the surface, a smooth scalar field that interpolates or approximates the constraints. Three types of constraints: point-value, point-gradient and iso-contour, are introduced to provide flexible control of the scalar field design. Furthermore, the framework also provides the user control over the region of influence and rate of influence decrease of the constraints, through parameter adjustment. We demonstrate that the scalar fields resulted from this framework can be used in several mesh applications such as skin deformation, region selection and curve drawing.
Spinal Astrocytic Activation Is Involved in a Virally-Induced Rat Model of Neuropathic Pain

Postherpetic neuralgia (PHN), the most common complication of herpes zoster (HZ), plays a major role in decreased life quality of HZ patients. However, the neural mechanisms underlying PHN remain unclear. Here, using a PHN rat model at 2 weeks after varicella zoster virus infection, we found that spinal astrocytes were dramatically activated. The mechanical allodynia and spinal central sensitization were significantly attenuated by intrathecally injected L-α-aminoadipate (astrocytic specific inhibitor) whereas minocycline (microglial specific inhibitor) had no effect, which indicated that spinal astrocyte but not microglia contributed to the chronic pain in PHN rat. Further study was taken to investigate the molecular mechanism of astrocyte-incudced allodynia in PHN rat at post-infection 2 weeks. Results showed that nitric oxide (NO) produced by inducible nitric oxide synthase mediated the development of spinal astrocytic activation, and activated astrocytes dramatically increased interleukin-1β expression which induced N-methyl-D-aspartic acid receptor (NMDAR) phosphorylation in spinal dorsal horn neurons to strengthen pain transmission. Taken together, these results suggest that spinal activated astrocytes may be one of the most important factors in the pathophysiology of PHN and “NO-Astrocyte-Cytokine-NMDAR-Neuron” pathway may be the detailed neural mechanisms underlying PHN. Thus, inhibiting spinal astrocytic activation may represent a novel therapeutic strategy for clinical management of PHN.
Virus Suspect Identified in Elephant Deaths

A research team reports on page 1171 that it has identified a virus that has killed at least eight juvenile Asian elephants at zoos. The virus, which is a distant relative of the herpesvirus that causes cold sores in humans, may have been transmitted to the Asian elephants from African elephants also kept in zoos. What9s more, the researchers suspect that Asian elephants harbor a virus that is fatal to their African cousins. By raising the possibility of fatal crossover infections, the work could influence how the world9s zoos take care of their elephants.
Terabit Transmission at 42.7-Gb/s on 50-GHz Grid Using Hybrid RZ-DQPSK and NRZ-DBPSK Formats Over 16$\,\times\,$ 80 km SSMF Spans and 4 Bandwidth-Managed ROADMs

We demonstrate for the first time the use of asymmetric-bandwidth interleaver-based reconfigurable optical add-drop multiplexer (ROADM) to transmit 42.7-Gb/s channels on a 50-GHz grid. Differential binary phase shift keyed (DBPSK) format was used on the wide passband side and differential quadrature phase shift keyed (DQPSK) format was used on the narrow passband side of the ROADM. 25 channels with an aggregate capacity of 1-Tb/s were transported over 1280-km of standard single-mode fiber (SSMF) including 4 ROADMs.
Convex Calibrated Surrogates for Hierarchical Classification

Hierarchical classification problems are multiclass supervised learning problems with a predefined hierarchy over the set of class labels. In this work, we study the consistency of hierarchical classification algorithms with respect to a natural loss, namely the tree distance metric on the hierarchy tree of class labels, via the usage of calibrated surrogates. We first show that the Bayes optimal classifier for this loss classifies an instance according to the deepest node in the hierarchy such that the total conditional probability of the subtree rooted at the node is greater than 1/2 . We exploit this insight to develop new consistent algorithm for hierarchical classification, that makes use of an algorithm known to be consistent for the "multiclass classification with reject option (MCRO)" problem as a subroutine. Our experiments on a number of benchmark datasets show that the resulting algorithm, which we term OvA-Cascade, gives improved performance over other state-of-the-art hierarchical classification algorithms.
The role of coping with disease in adherence to treatment regimen and disease control in type 1 and insulin treated type 2 diabetes mellitus.

BACKGROUND Coping is defined as the behavioral and cognitive efforts used in an attempt to deal with stressful events. The objective of this study was to explore the relationship between coping with diabetes and the following outcome variables in type 1 and insulin treated type 2 diabetes mellitus: glycemic control, microangiopathic complications, adherence to self monitoring of blood glucose, adherence to insulin injections, and adherence to diet. METHODS Subjects were 196 insulin treated adult diabetes patients visiting an outpatient clinic at a government university hospital in Istanbul, Turkey. Coping with disease was measured with the Turkish version of the Diabetes Coping Measure and adherence to treatment regimen was measured with a questionnaire adapted from the subscales of the Summary of Diabetes Self-Care Activities Questionnaire. Data on patients' HbA(1c) levels and severity of microangiopathic complications were obtained from their medical records. RESULTS Partial correlations controlling for background variables suggested that coping was a good predictor of outcome for both type 1 and insulin treated type 2 diabetes mellitus. These associations were more pronounced for type 1 patients when compared to type 2 patients. Regressing the outcome variables on the two second-order coping factors (obtained by a factor analysis) also supported the hypothesis that coping is an important construct in explaining the outcome variables. Finally, the effect of coping on HbA(1c) was only partially mediated by adherence. CONCLUSION Coping with diabetes-related issues is an important factor in both types of diabetes, with type 1 patients showing slightly stronger associations. Therefore, training and education programs for diabetic adults might benefit from including a component that is aimed at improving coping with issues specific to diabetes.