Miracle-dz/UniFAR-FTUs huggingface dataset:
Development and external validation of a nomogram for overall survival after curative resection in serosa-negative, locally advanced gastric cancer.

BACKGROUND Few nomograms can predict overall survival (OS) after curative resection of advanced gastric cancer (AGC), and these nomograms were developed using data from only a few large centers over a long time period. The aim of this study was to develop and externally validate an elaborative nomogram that predicts 5-year OS after curative resection for serosa-negative, locally AGC using a large amount of data from multiple centers in Japan over a short time period (2001-2003). PATIENTS AND METHODS Of 39 859 patients who underwent surgery for gastric cancer between 2001 and 2003 at multiple centers in Japan, we retrospectively analyzed 5196 patients with serosa-negative AGC who underwent Resection A according to the 13th Japanese Classification of Gastric Carcinoma. The data of 3085 patients who underwent surgery from 2001 to 2002 were used as a training set for the construction of a nomogram and Web software. The data of 2111 patients who underwent surgery in 2003 were used as an external validation set. RESULTS Age at operation, gender, tumor size and location, macroscopic type, histological type, depth of invasion, number of positive and examined lymph nodes, and lymphovascular invasion, but not the extent of lymphadenectomy, were associated with OS. Discrimination of the developed nomogram was superior to that of the TNM classification (concordance indices of 0.68 versus 0.61; P < 0.001). Moreover, calibration was accurate. CONCLUSIONS We have developed and externally validated an elaborative nomogram that predicts the 5-year OS of postoperative serosa-negative AGC. This nomogram would be helpful in the assessment of individual risks and in the consideration of additional therapy in clinical practice, and we have created freely available Web software to more easily and quickly predict OS and to draw a survival curve for these purposes.
Effect of thermal stress of short duration on the red blood cell parameters of Barbus balcanicus Kotlik , Tsigenopulos , Rab , Berrebi , 2002

In this study, red blood cell parameters of Barbus balcanicus Kotlik, Tsigenopulos, Rab, Berrebi, 2002 subjected to acute thermal stress were investigated. Fish were caught by electro fishing in the Suturlija river, a small tributary of the river Vrbas (N latitude 44 ̊44' 38 ̋, E longitude 17 ̊ 09' 10 ̋) in summer (July) and transported to the laboratory. Fish were randomly distributed in four aquaria of 30 L each. In all the four aquaria, the water temperature was continuously kept at 19°C by appropriate devices. After period of adaptation (three weeks), half of the fish (24) were used as a control group while the other 24 were subjected to thermal stress by raising the water temperature to 29°C (10°C increase) in 60 min. In both control and thermally treated, fish blood was collected by heart puncture according to “Animal welfare act“. Analyses were performed with native blood, without addition of any anticoagulant and the values of red blood cell count (RBC), haemoglobin concentration, packed cell volume (PCV), Corpuscular Volume (MCV), Mean Corpuscular Haemoglobin (MCH) and Mean Corpuscular Haemoglobin Concentration (MCHC) were determined. In the thermally treated fish, the values of PCV and MCV increased (p = 0.0003 and p = 0.0147 respectively), and those of MCHC decreased substantially (p = 0.0001).
PIPE-chipSAD: A Pipeline for the Analysis of High Density Arrays of Bacterial Transcriptomes

PIPE-chipSAD is a pipeline for bacterial transcriptome studies based on high-density microarray experiments. The main algorithm chipSAD, integrates the analysis of the hybridization signal with the genomic position of probes and identifies portions of the genome transcribing for mRNAs. The pipeline includes a procedure, align-chipSAD, to build a multiple alignment of transcripts originating in the same locus in multiple experiments and provides a method to compare mRNA expression across different conditions. Finally, the pipeline includes anno-chipSAD a method to annotate the detected transcripts in comparison to the genome annotation. Overall, our pipeline allows transcriptional profile analysis of both coding and non-coding portions of the chromosome in a single framework. Importantly, due to its versatile characteristics, it will be of wide applicability to analyse, not only microarray signals, but also data from other high throughput technologies such as RNA-sequencing. The current PIPE-chipSAD implementation is written in Python programming language and is freely available at https://github.com/silviamicroarray/chipSAD.
Thymic recovery after allogeneic hematopoietic cell transplantation with non-myeloablative conditioning is limited to patients younger than 60 years of age

Background Long-term immune recovery in older patients given hematopoietic cell transplantation after non-myeloablative conditioning remains poorly understood. This prompted us to investigate long-term lymphocyte reconstitution and thymic function in 80 patients given allogeneic peripheral blood stem cells after non-myeloablative conditioning. Design and Methods Median age at transplant was 57 years (range 10–71). Conditioning regimen consisted of 2 Gy total body irradiation (TBI) with (n=46) or without (n=20) added fludarabine, 4 Gy TBI with fludarabine (n=6), or cyclophosphamide plus fludarabine (n=8). Stem cell sources were unmanipulated (n=56), CD8-depleted (n=19), or CD34-selected (n=5) peripheral blood stem cells. Immune recovery was assessed by signal-joint T-cell receptor excision circle quantification and flow cytometry. Results Signal-joint T-cell receptor excision circle levels increased from day 100 to one and two years after transplantation in patients under 50 years of age (n=23; P=0.02 and P=0.04, respectively), and in those aged 51–60 years (n=35; P=0.17 and P=0.06, respectively), but not in patients aged over 60 (n=22; P=0.3 and P=0.3, respectively). Similarly, CD4+CD45RA+ (naïve) T-cell counts increased from day 100 to one and two years after transplantation in patients aged 50 years and under 50 (P=0.002 and P=0.02, respectively), and in those aged 51–60 (P=0.4 and P=0.001, respectively), but less so in patients aged over 60 (P=0.3 and P=0.06, respectively). In multivariate analyses, older patient age (P<0.001), extensive chronic GVHD (P<0.001), and prior (resolved) extensive chronic graft-versus-host disease (P=0.008) were associated with low signal-joint T-cell receptor excision circle levels one year or more after HCT. Conclusions In summary, our data suggest that thymic neo-generation of T cells occurred from day 100 onwards in patients under 60 while signal-joint T-cell receptor excision circle levels remained low for patients aged over 60. Further, chronic graft-versus-host disease had a dramatic impact on thymic function, as observed previously in patients given grafts after myeloablative conditioning.
Active-State Model of a Dopamine D2 Receptor - Gαi Complex Stabilized by Aripiprazole-Type Partial Agonists

Partial agonists exhibit a submaximal capacity to enhance the coupling of one receptor to an intracellular binding partner. Although a multitude of studies have reported different ligand-specific conformations for a given receptor, little is known about the mechanism by which different receptor conformations are connected to the capacity to activate the coupling to G-proteins. We have now performed molecular-dynamics simulations employing our recently described active-state homology model of the dopamine D2 receptor-Gαi protein-complex coupled to the partial agonists aripiprazole and FAUC350, in order to understand the structural determinants of partial agonism better. We have compared our findings with our model of the D2R-Gαi-complex in the presence of the full agonist dopamine. The two partial agonists are capable of inducing different conformations of important structural motifs, including the extracellular loop regions, the binding pocket and, in particular, intracellular G-protein-binding domains. As G-protein-coupling to certain intracellular epitopes of the receptor is considered the key step of allosterically triggered nucleotide-exchange, it is tempting to assume that impaired coupling between the receptor and the G-protein caused by distinct ligand-specific conformations is a major determinant of partial agonist efficacy.
Minimizing simultaneous switching noise (SSN) using modified odd/even bus invert method

In high speed digital circuits, the inductive effect is more dominant compared to capacitive effect. In particular, as the technology is shrinking, the spacing between interconnects becomes less which increases simultaneous switching noise (SSN) or M(di/dt) noise. So earlier methods proposed which concentrate on reducing capacitive effect do not hold good. This paper proposes a modified odd/even bus invert scheme, which reduces the simultaneous switching activity, thereby improving the signal integrity. The performance of the proposed coding scheme has been tested on various benchmarks and it is found that SSN or M(di/dt) is reduced by 28% compared to data transmitted unencoded. The proposed codec has been designed and it has been found that power overhead is 3.3%.
Constraints from the Hubble Deep Field on High-Redshift Quasar Models

High-resolution, deep-imaging surveys are instrumental in setting constraints on semianalytical structure formation models in cold dark matter (CDM) cosmologies. We show here that the lack of unresolved B-band "dropouts" with V>25 mag in the Hubble Deep Field appears to be inconsistent with the number of "miniquasars" expected if massive black holes form with a constant universal efficiency in all CDM halos. To reconcile the models with the data, a mechanism is needed that suppresses the formation of active nuclei in halos with circular velocities vcirc≲50-75 km s-1. This feedback naturally arises because of the photoionization heating of the gas by the UV background. We consider several alternative effects that would help reducing the number of miniquasars and find that these cannot alone account for the observed lack of detections. If reddening by dust can be neglected at early epochs, consistency with the optical data also requires that the luminous extent of dwarf galaxies at high redshifts be larger than a few percent of the virial radii of their dark matter halos, in order not to overpredict the number of pointlike B-band dropouts. Future deep observations in the J and H bands with NICMOS might reveal several z≳5 objects per field or provide even stronger constraints on the models than existing B, V, and I data.
A semi-supervised approach for author disambiguation in KDD CUP 2013

Name disambiguation, which aims to identify multiple names which correspond to one person and same names which refer to different persons, is one of the most important basic problems in many areas such as natural language processing, information retrieval and digital libraries. Microsoft academic search data in KDD Cup 2013 Track 2 task brings one such challenge to the researchers in the knowledge discovery and data mining community. Besides the real-world and large-scale characteristic, the Track 2 task raises several challenges: (1) Consideration of both synonym and polysemy problems; (2) Existence of huge amount of noisy data with missing attributes; (3) Absence of labeled data that makes this challenge a cold start problem. In this paper, we describe our solution to Track 2 of KDD Cup 2013. The challenge of this track is author disambiguation, which aims at identifying whether authors are the same person by using academic publication data. We propose a multi-phase semi-supervised approach to deal with the challenge. First, we preprocess the dataset and generate features for models, then construct a coauthor-based network and employ community detection to accomplish first-phase disambiguation task, which handles the cold-start problem. Second, using results in first phase, we use support vector machine and various other models to utilize noisy data with missing attributes in the dataset. Further, we propose a self-taught procedure to solve ambiguity in coauthor information, boosting performance of results from other models. Finally, by blending results from different models, we finally achieves 6th place with 0.98717 mean F-score on public leaderboard and 7th place with 0.98651 mean F-score on private leaderboard.
PI3K-GLUT4 Signal Pathway Associated with Effects of EX-B3 Electroacupuncture on Hyperglycemia and Insulin Resistance of T2DM Rats

Objectives. To explore electroacupuncture's (EA's) effects on fasting blood glucose (FBG) and insulin resistance of type 2 diabetic mellitus (T2DM) model rats and give a possible explanation for the effects. Method. It takes high fat diet and intraperitoneal injection of streptozotocin (STZ, 30 mg/kg) for model preparation. Model rats were randomly divided into T2DM Model group, EA weiwanxiashu (EX-B3) group, and sham EA group (n = 12/group). EA (2 Hz continuous wave, 2 mA, 20 min/day, 6 days/week, 4 weeks) was applied as intervention. FBG, area under curve (AUC) of oral glucose tolerance test (OGTT), insulin resistance index (HOMA-IR), pancreatic B cell function index (HOMA-B), skeletal muscle phosphorylated phosphatidylinositol-3-kinase (PI3K), glucose transporter 4 (GLUT4), and membrane GLUT4 protein expression were measured. Results. EA weiwanxiashu (EX-B3) can greatly upregulate model rat's significantly reduced skeletal muscle PI3K (Y607) and membrane GLUT4 protein expression (P < 0.01), effectively reducing model rats' FBG and AUC of OGTT (P < 0.01). The effects are far superior to sham EA group. Conclusion. EA weiwanxiashu (EX-B3) can upregulate skeletal muscle phosphorylated PI3K protein expression, to stimulate membrane translocation of GLUT4 and thereby increase skeletal muscle glucose intake to treat T2DM.
CRITERIA FOR D-CONTINUITY

Bernoullicity is the strongest mixing property that a measuretheoretic dynamical system can have. This is known to be intimately connected to the so-called d̄ metric on processes, introduced by Ornstein. In this paper, we consider families of measures arising in a number of contexts and give conditions under which the measures depend d̄-continuously on the parameters. At points where there is d̄-continuity, it is often straightforward to establish that the measures have the Bernoulli property. Introduction One of the most standard examples of a measure-preserving transformation in ergodic theory is that of a Bernoulli shift. To construct these, one starts with a finite set S equipped with a measure m and defines the shift transformation T on the space X = SZ equipped with the measure mZ, the direct product of copies of m indexed by the integers. These transformations model the simple situation which occurs in probability theory of having a sequence of independent identically distributed random variables (Bernoulli trials). For this reason, Bernoulli shifts are often referred to as the most random possible dynamical systems. A fundamental question which often arises in ergodic theory is when a pair of measure-preserving transformations are measure-theoretically isomorphic. These questions are known to be hard, and until the mid 1970s, the results were few. It then came as a great surprise when Ornstein showed in a series of papers (collected together as [11] see also [16]) that there is a very simple classification of Bernoulli shifts (namely, that two Bernoulli shifts are isomorphic if and only if they have the same entropy) and gave verifiable conditions for checking whether other systems are also isomorphic to Bernoulli shifts. This resulted in an explosion of work, showing that a large number of ‘naturally occurring’ measure-preserving systems were isomorphic to Bernoulli shifts. When this is the case, it is often said that the system has the Bernoulli property. Some of the results in this paper fall into this category. A convenient way of establishing Bernoullicity in our context is provided by means of the d̄ distance introduced by Ornstein. A useful description of this is offered by joinings (see Rudolph’s book [14] for details). A joining of (X, ν1) and (X, ν2) is a shift-invariant measure on X ×X with the property that μ(A×X) = ν1(A) and μ(X × B) = ν2(B) for any measurable subsets A and B of X . Writing Received by the editors March 7, 1996 and, in revised form, September 18, 1996. 1991 Mathematics Subject Classification. Primary 28D05, 60G10.
Methods for solving problems in financial portfolio construction, index tracking and enhanced indexation

The focus of this thesis is on index tracking that aims to replicate the movements of an index of a specific financial market. It is a form of passive portfolio (fund) management that attempts to mirror the performance of a specific index and generate returns that are equal to those of the index, but without purchasing all of the stocks that make up the index. Additionally, we consider the problem of out-performing the index Enhanced Indexation. It attempts to generate modest excess returns compared to the index. Enhanced indexation is related to index tracking in that it is a relative return strategy. One seeks a portfolio that will achieve more than the return given by the index (excess return). In the first approach, we propose two models for the objective function associated with choice of a tracking portfolio, namely; minimise the maximum absolute difference between the tracking portfolio return and index return and minimise the average of the absolute differences between tracking portfolio return and index return. We illustrate and investigate the performance of our models from two perspectives; namely, under the exclusion and inclusion of fixed and variable costs associated with buying or selling each stock. The second approach studied is that of using Quantile regression for both index tracking and enhanced indexation. We present a mixed-integer linear programming of these problems based on quantile regression. The third approach considered is on quantifying the level of uncertainty associated with the portfolio selected. The quantification of uncertainty is of importance as this provides investors with an indication of the degree of risk that can be expected as a result of holding the selected portfolio over the holding period. Here a bootstrap approach is employed to quantify the uncertainty of the portfolio selected from our quantile regression model. Certificate of Originality “I hereby certify that the work presented in this thesis is my original research and has not been presented for a higher degree at any other university or institute”. Hakim Mezali
A community-based intervention for improving health-seeking behavior among sexual violence survivors: a controlled before and after design study in rural Tanzania

Background Despite global recognition that sexual violence is a violation of human rights, evidence still shows it is a pervasive problem across all societies. Promising community intervention studies in the low- and middle-income countries are limited. Objective This study assessed the impact of a community-based intervention, focusing on improving the community's knowledge and reducing social acceptability of violence against women norms with the goal to prevent and respond to sexual violence. Design The strategies used to create awareness included radio programs, information, education communication materials, and advocacy meetings with local leaders. The intervention took place in Morogoro region in Tanzania. The evaluation used a quasi-experimental design including cross-sectional surveys at baseline (2012) and endline (2014) with men and women aged 18–49 years. Main outcome measures were number of reported rape cases at health facilities and the community's knowledge and attitudes toward sexual violence. Results The number of reported rape events increased by more than 50% at health facilities during the intervention. Knowledge on sexual violence increased significantly in both areas over the study period (from 57.3 to 80.6% in the intervention area and from 55.5 to 71.9% in the comparison area; p<0.001), and the net effect of the intervention between the two areas was statistically significant (6.9, 95% CI 0.2–13.5, p=0.03). There was significant improvement in most of the attitude indicators in the intervention area, but not in the comparison area. However, the intervention had no significant effect on the overall scores of acceptance attitudes in the final assessment when comparing the two areas (−2.4, 95% CI: −8.4 to 3.6, p=0.42). Conclusions The intervention had an effect on some indicators on knowledge and attitudes toward sexual violence even after a short period of intervention. This finding informs the public health practitioners of the importance of combined strategies in achieving changes.
ANALYTICAL DYNAMICAL MODELS FOR DOUBLE POWER-LAW GALACTIC NUCLEI

Motivated by the finding that the observed surface brightness profile of many galactic nuclei are well fit by double-power-laws, we explore a range of spherical self-consistent dynamical models with this light profile. We find that the corresponding deprojected volume density profile, phase space density and line-of-sight velocity distribution of these models are well fit by simple analytic approximations. We illustrate the application of these models by fitting a sample of about 25 galactic nuclei observed by Hubble Space Telescope. We give the derived volume density, phase space density, velocity dispersion and line profile parameters in tables. The models are useful for predicting kinematic properties of these galaxies for comparison with future observations. They can also be easily applied to seed N-body simulations of galactic nuclei with realistic density profiles for studying the evolution of these systems.
The Role of Income Effects in Early Retirement

We provide a long term perspective on the individual retirement behavior and on the future of retirement by emphasizing the role of (negative) income effects. We consider a political economic theoretical framework, with actuarial "fair" and "unfair" early retirement schemes, and derive a political equilibrium with positive social security contribution rates and early retirement. A reduction in the wages in youth, consistent with the recent labor market trends since the massive introduction of temporary jobs, induces workers to postpone retirement, and — in the "unfair" system — leads to lower contribution rates. A reduction in the growth rate of the economy has opposite effects on the retirement decisions, leading — in the "unfair" system — to more early retirement. Aging induces a negative income effect, but has also an opposite political effects on social security contributions and retirement decisions. For an actuarial "fair" social security system, we provide conditions for the political effect to dominate; in an "unfair" scheme, numerical simulations confirm a slight predominance of the political effect, as contribution rates increase. These results may shed some light on the future of early retirement in aging societies.
Options, Option Repricing and Severance Packages in Managerial Compensation: Their Effects on Corporate Risk

While stock options are commonly used in managerial compensation to provide desirable incentives, their adverse effects have not been widely appreciated. We show that a call-type contract creates incentives to distort the choice of investment risk. Relative to the risk level that maximizes firm value, a call option contract can induce too much or too little corporate risk-taking, depending on managerial risk aversion and the underlying investment technology. We show that including additional compensation features of option repricing and/or severance packages has desirable countervailing effects on managerial choice of corporate risk policies. We argue that lookback call options are analogous to the observed practice of option repricing, and put options are analogous to severance packages. Such complex option-like features in managerial contracts can induce risk policies that increase shareholder wealth.