Miracle-dz/UniFAR-FTUs huggingface dataset:
A multicenter, open-label, pilot study evaluating the functionality of an integrated call center for a digital medicine system to optimize monitoring of adherence to oral aripiprazole in adult patients with serious mental illness

Background Medication nonadherence is common in the treatment of serious mental illness (SMI) and leads to poor outcomes. The digital medicine system (DMS) objectively measures adherence with oral aripiprazole in near-real time, allowing recognition of adherence issues. This pilot study evaluated the functionality of an integrated call center in optimizing the use of the DMS. Materials and methods An 8-week, open-label, single-arm trial at four US sites enrolled adults with bipolar I disorder, major depressive disorder, and schizophrenia on stable oral aripiprazole doses and willing to use the DMS (oral aripiprazole + ingestible event marker [IEM], IEM-detecting skin patch, and software application). Integrated call-center functionality was assessed based on numbers and types of calls. Ingestion adherence with prescribed treatment (aripiprazole + IEM) during good patch wear and proportion of time with good patch wear (days with ≥80% patch data or detected IEM) were also assessed. Results All enrolled patients (n=49) used the DMS and were included in analyses; disease duration overall approached 10 years. For a duration of 8 weeks, 136 calls were made by patients, and a comparable 160 calls were made to patients, demonstrating interactive communication. The mean (SD) number of calls made by patients was 2.8 (3.5). Approximately half of the inbound calls made by patients occurred during the first 2 weeks and were software application- or patch-related. Mean ingestion adherence was 88.6%, and corresponding good patch wear occurred on 80.1% of study days. Conclusion In this pilot study, the integrated call center facilitated DMS implementation in patients with SMI on stable doses of oral aripiprazole. In clinical practice, the call center and the DMS will facilitate objective measurement of adherence and potentially improve rates of adherence in patients with SMI.
Protective effects of cynaroside against H2O2‐induced apoptosis in H9c2 cardiomyoblasts

Flavonoids with potent anti‐oxidative effects are the major effective components in traditional herbal medicine used in treating cardiovascular diseases. Cynaroside is a flavonoid compound that exhibits anti‐oxidative capabilities. However, little is known about its effect on oxidative injury to cardiac myocytes and the underlying mechanisms. This study was designed to investigate the protective effects of cynaroside against H2O2‐induced apoptosis in H9c2 cardiomyoblasts. H9c2 cells were pretreated with cynaroside for 4 h before exposure to 150 µM H2O2 for 6 h. H2O2 treatment caused severe injury to the H9c2 cells, which was accompanied by apoptosis, as revealed by analysis of cell nuclear morphology, through Annexin V FITC/PI staining and caspase proteases activation. Cynaroside pretreatment significantly reduced the apoptotic rate by enhancing the endogenous anti‐oxidative activity of superoxide dismutase, glutathione peroxidase, and catalase, thereby inhibiting intracellular reactive oxygen species (ROS) generation. Moreover, cynaroside moderated H2O2‐induced disruption of mitochondrial membrane potential, increased the expression of anti‐apoptotic protein Bcl‐2 while decreased the expression of pro‐apoptotic protein Bax, and thereby inhibited the release of apoptogenic factors (cytochrome c and smac/Diablo) from mitochondria in H9c2 cells. Our data also demonstrated that cynaroside pretreatment showed an inhibitory effect on the H2O2‐induced increase in c‐Jun N‐terminal kinase (JNK) and P53 protein expression. These results suggest that cynaroside prevents H2O2‐induced apoptosis in H9c2 cell by reducing the endogenous production of ROS, maintaining mitochondrial function, and modulating the JNK and P53 pathways. J. Cell. Biochem. 112: 2019–2029, 2011. © 2011 Wiley‐Liss, Inc.
Three essays on unemployment insurance in the 21st century

OF DISSERTATION THREE ESSAYS ON UNEMPLOYMENT INSURANCE IN THE 21ST CENTURY My dissertation consists of three essays focusing on unemployment insurance (UI) and how it affects recipients. The first essay examines how UI generosity affects the search intensity of recipients through matching American Time Use Survey respondents to all of their observations in the Current Population Survey (CPS), the population from which they are drawn. Earnings from the CPS are then run through a benefit calculator that determines eligibility and benefit amounts which are used to determine how UI generosity affects search times. The second essay uses the Survey of Income and Program Participation to examine how lesser known policies affecting UI eligibility of workers with limited earnings histories, part-time workers, voluntary job leavers, and expanding benefit amounts for individuals with children affect unemployment duration. The third essay examines how liquidity constraints affect the consumption smoothing benefits of UI. Using the Panel Study of Income Dynamics from 1968-2012, I find that the consumption smoothing benefits of UI that past studies have found are primarily concentrated on the 27% of households that do not have other means of smoothing consumption. For these households, a 10 percentage-point increase in the replacement rate reduces the decline in consumption by between 3.5-4.9% using food consumption and 1.5-2.1% using imputed total consumption.
(Nearly) Efficient Algorithms for the Graph Matching Problem on Correlated Random Graphs

We give a quasipolynomial time algorithm for the graph matching problem (also known as noisy or robust graph isomorphism) on correlated random graphs. Specifically, for every $\gamma>0$, we give a $n^{O(\log n)}$ time algorithm that given a pair of $\gamma$-correlated $G(n,p)$ graphs $G_0,G_1$ with average degree between $n^{\varepsilon}$ and $n^{1/153}$ for $\varepsilon = o(1)$, recovers the "ground truth" permutation $\pi\in S_n$ that matches the vertices of $G_0$ to the vertices of $G_n$ in the way that minimizes the number of mismatched edges. We also give a recovery algorithm for a denser regime, and a polynomial-time algorithm for distinguishing between correlated and uncorrelated graphs. Prior work showed that recovery is information-theoretically possible in this model as long the average degree was at least $\log n$, but sub-exponential time algorithms were only known in the dense case (i.e., for $p > n^{-o(1)}$). Moreover, "Percolation Graph Matching", which is the most common heuristic for this problem, has been shown to require knowledge of $n^{\Omega(1)}$ "seeds" (i.e., input/output pairs of the permutation $\pi$) to succeed in this regime. In contrast our algorithms require no seed and succeed for $p$ which is as low as $n^{o(1)-1}$.
The value of information in centralized school choice systems

Strategy-proofness and assurance of a fair matching are desirable qualities for school choice mechanisms. Although these qualities are theoretical properties of the unrestricted-list deferred acceptance mechanism (DA), it has proven to be hard to go without list-size restrictions in practice. This paper shows how a simple modification to the restricted-list DA, in which students are provided more information about vacancies and offered higher-value options in the event of rejection, can mitigate uncertainty and yield matches very close to what would be obtained under the unrestricted-list DA. I estimate an application-portfolio choice model using administrative data from Tunisia, where a sequential implementation of the DA is used to assign high-school graduates to universities. This sequential implementation creates quasi-experimental variation that allows to separate the identification of students’ preferences for programs from their expectations about their admission probabilities. Counterfactual simulations show that the average student’s expected ex post utility is significantly lower when assignments are made using the standard restricted-list DA than what it would be in the unrestricted-list DA match. Using a sequential implementation, as is done in Tunisia, instead of the standard restricted-list DA, can reduce this welfare loss by 90%. ∗Email address: mluflade@sas.upenn. edu †I am extremely grateful to Meryam Zaiem whose insights about the context, help with obtaining the data, and encouragement have been critical to the realization of this project. I am grateful to Arnaud Maurel, Peter Arcidiacono, Joe Hotz, and Matt Masten for help and suggestions, as well as continuous support and encouragement. I thank Atila Abdulkadiroğlu, Eli Liebman, Pedro Mira, Derek Neal, Aviv Nevo, Seth Sanders, Modibo Sidibé, Petra Todd, and the participants at the Duke Labor and Microeconometrics workshops and at many other seminars, for very helpful comments and discussions. I thank the Ministry of Higher Education of Tunisia for providing the data. All errors are mine.
A Primer on Alternative Risk Premia

The concept of alternative risk premia can be viewed as an extension of the factor investing approach. Factor investing is a term that is generally dedicated to long-only equity risk factors. A typical example is the value equity strategy. Alternative risk premia designate non-traditional risk premia other than long exposure to equities and bonds. They may concern equities, rates, credit, currencies or commodities and correspond to long/short portfolios. For instance, the value strategy can be extended to credit, currencies and commodities. This paper provides an overview of the different alternative risk premia to be found in the academic and professional spheres. Using a database of commercial indices, we estimate the generic cumulative returns of 59 alternative risk premia in order to analyze their risk, diversification power and payoff function. From this, it is clear that the term "alternative risk premia" encompasses two different types of risk factor: skewness risk premia and market anomalies. We then reconsider portfolio allocation in light of this framework. Indeed, we show that skewness aggregation is considerably more complex than volatility aggregation, and we illustrate that the volatility risk measure is less appropriate and pertinent when managing a portfolio with these risk premia. The development of alternative risk premia shall also affect the risk/return analysis of non-linear strategies, e.g. hedge fund strategies. In particular, using alternative risk factors instead of traditional risk factors leads to an extension of the alternative beta framework. Therefore, we apply the previously estimated risk premia to a universe of hedge fund indices. To that end, we develop a model selection based on the lasso regression to identify the most pertinent risk premia for each hedge fund strategy. It appears that many traditional risk factors, with the exception of long equity and credit exposure on developed markets, vanish when we include alternative risk premia.
The impact of ESG disclosures and institutional ownership on market information asymmetry

Abstract This paper investigates the impact of ESG disclosures and institutional ownership on market information asymmetry for 683 firms listed on the New York Stock Exchange for years 2007–2011. Overall, the results suggest that there is a statistically significant negative relationship between ESG disclosures and bid-ask spread and that the presence of institutional investors reduces market information asymmetry. However, it is further established in this paper that a relatively higher level of institutional ownership may attenuate this effect because there is a tendency for institutional owners to exploit private ESG information gained through their position.
Effect of High Copy Number of HER2 Associated With Polysomy 17 on HER2 Protein Expression in Invasive Breast Carcinoma

HER2 gene amplification by fluorescence in situ hybridization and protein expression by immunohistochemistry (IHC) have been used for prognosis and guiding treatment of invasive ductal carcinoma of the breast with trastuzumab. Accurate evaluation of HER2 status is important in the management of patients with candidacy for the HER2-targeting therapy. Despite previous studies, effects of polysomy of chromosome 17, at which HER2 is located, on HER2 protein expression remains controversial. In this study, we calculated the average copy numbers of HER2 and chromosome 17 (CEP17) per nucleus in 109 cases of invasive breast carcinoma and analyzed their correlations with the HER2/CEP17 ratio and protein expression. As expected, there were close correlations between HER2 protein expression and the HER2/CEP17 ratio (CC: 0.49, P<0.001), along with the HER2 copy number per nucleus (CC: 0.48, P<0.001) and between the CEP17 copy number per nucleus and the HER2 copy number per nucleus (CC: 0.45, P<0.001). Correlation between the CEP17 copy number per nucleus and the HER2/CEP17 ratio was not significant (CC: 0.2, P>0.05). There was a weak, but statistically insignificant, correlation between the CEP17 copy number per nucleus and HER2 protein expression by IHC (CC: 0.26, P>0.05). The cases were then grouped on the basis of the amplification of the HER2 gene by fluorescence in situ hybridization. In the cases that showed no amplification, there was a significantly higher CEP17 copy number per nucleus in cases with strong HER2 protein expression (2.99) when compared with cases with weak (2.39) or absent (1.86) expression. In conclusion, a high HER2 gene copy number-associated polysomy 17 is a significant contributing factor in HER2 protein overexpression in unamplified invasive breast carcinomas. Cases without HER2 amplification, but carrying polysomy 17, should be further evaluated for HER2 protein overexpression by IHC. Those with polysomy 17-associated HER2 protein overexpression, like any other IHC+ ones, should be eligible candidates for trastuzumab therapy.
Measurement of motility of Helicobacter pylori, Campylobacter jejuni, and Escherichia coli by real time computer tracking using the Hobson BacTracker.

AIMS: (1) To make precise measurements and comparisons of various aspects of motility of three gastrointestinal pathogens, Helicobacter pylori, Campylobacter jejuni, and Escherichia coli, in log phase growth; (2) to provide background information on motility data to study the influence of pH, viscosity, and chemotactic factors, thereby gaining a better understanding of bacterial pathogenesis. METHODS: Computer image processing technology and phase contrast microscopy (Hobson BacTracker) were used to measure several indices of bacterial motility in real time. Ten clinical isolates of each species in log phase liquid culture were studied. RESULTS: C jejuni moved fastest, with a median curvilinear velocity (CLV) of 38.76 microns/s (range 29.08 to 52.82). Next was H pylori, median CLV 25.02 microns/s (range 12.07 to 29.07). E coli was the slowest, median CLV 12.73 microns/s (range 8.20 to 18.04). The straight line velocities showed similar trends. Measurement of track linearity (TL) showed that C jejuni moved the straightest (TL 60.3%), H pylori moved in wide circles (TL 28.7%), and E coli showed spinning movement without much linear displacement (TL 18.3%). There were significant differences in these three variables between the species studied, but no significant differences in measurements of time and frequency of halts between movement runs. CONCLUSIONS: The BacTracker provides a useful technical aid for measuring several indices of bacterial motility objectively, reproducibly, and precisely, which is difficult to achieve without computer assistance. Accurate quantification of motility provides a basis for studying the factors which influence bacterial motility. It can provide phenotypic measurements of the effect of flagellar gene depletion.
Epidemiology of Echinococcus granulosus in Arbil province, northern Iraq, 1990–1998

Abstract During the period 1990–1998, 99 cases of human cystic hydatidosis (12.4 cases per year) were surgically treated at the two main hospitals in Arbil province, northern Iraq, and from this the human occurence for the province was estimated to be 2 per 100,000 inhabitants. In the same area, 1270 sheep, 550 goats and 320 cattle were examined at slaughter for hydatid cysts and prevalence rates were found to be 15.0%, 6.2% and 10.9%, respectively. A decreasing tendency in livestock prevalences was found towards the end of the study period. As in humans, most of the hydatid cysts in livestock were located in the liver. Fertility of sheep cysts, i.e. those containing protoscoleces, was found to be significantly higher (64%) than that of goats (35.7%) and cattle (29.8%). The percentage of fertile cysts containing viable protoscoleces varied between 63 and 82% in the livers and between 72 and 79% in the lungs of the different animal species. A total of 97 stray dogs were examined post-mortem in the years 1991, 1992 and 1998, and Echinococcus granulosus worms were found in the intestines of 48 dogs (49.5%). High worm burdens (> 1000) were observed in 37% of the dogs, medium worm burdens (200–1000) in 41%, and low worm burdens (< 200) in 22%. In 1998, the prevalence of canine echinococcosis (24.3%) was found to be significantly lower than in 1991 (70.4%) and 1992 (60.6%). The prevalence of human hydatidosis did not differ significantly over the years, but the study confirmed that hydatidosis is endemic in northern Iraq, and that housewives, labourers and farmers appear to be at the greatest risk of infection.
Effects of aeration and natural zeolite on ammonium removal during the treatment of sewage by mesocosm-scale constructed wetlands

ABSTRACT The objective was to evaluate the effects of intermittent artificial aeration cycles and natural zeolite as a support medium, in addition to the contribution of plants (Schoenoplectus californicus) on NH4+–N removal during sewage treatment by Constructed Wetlands (CW). Two lines of Mesocosm Constructed Wetland (MCW) were installed: (a) gravel line (i.e. G-Line) and (b) zeolite line (i.e. Z-Line). Aeration increased the NH4+–N removal efficiency by 20–45% in the G-Line. Natural zeolite increased the NH4+–N removal efficiency by up to 60% in the Z-Line. Plants contributed 15–30% of the NH4+–N removal efficiency and no difference between the G-Line and the Z-Line. Conversely, the NH4+–N removal rate was shown to only increase with the use of natural zeolite. However, the MCW with natural zeolite, the NH4+–N removal rate showed a direct relationship only with the NH4+–N influent concentration. Additionally, relationship between the oxygen, energy and area regarding the NH4+–N removal efficiency was established for 2.5–12.5 gO2/(kWh-m2) in the G-Line and 0.1–2.6 gO2/(kWh-m2) in the Z-Line. Finally, it was established that a combination of natural zeolite as a support medium and the aeration strategy in a single CW could regenerate the zeolite’s adsorption sites and maintain a given NH4+–N removal efficiency over time.
Mycobacterium tuberculosis-induced miR-155 subverts autophagy by targeting ATG3 in human dendritic cells

Autophagy is a primordial eukaryotic pathway, which provides the immune system with multiple mechanisms for the elimination of invading pathogens including Mycobacterium tuberculosis (Mtb). As a consequence, Mtb has evolved different strategies to hijack the autophagy process. Given the crucial role of human primary dendritic cells (DC) in host immunity control, we characterized Mtb-DC interplay by studying the contribution of cellular microRNAs (miRNAs) in the post-transcriptional regulation of autophagy related genes. From the expression profile of de-regulated miRNAs obtained in Mtb-infected human DC, we identified 7 miRNAs whose expression was previously found to be altered in specimens of TB patients. Among them, gene ontology analysis showed that miR-155, miR-155* and miR-146a target mRNAs with a significant enrichment in biological processes linked to autophagy. Interestingly, miR-155 was significantly stimulated by live and virulent Mtb and enriched in polysome-associated RNA fraction, where actively translated mRNAs reside. The putative pair interaction among the E2 conjugating enzyme involved in LC3-lipidation and autophagosome formation-ATG3-and miR-155 arose by target prediction analysis, was confirmed by both luciferase reporter assay and Atg3 immunoblotting analysis of miR-155-transfected DC, which showed also a consistent Atg3 protein and LC3 lipidated form reduction. Late in infection, when miR-155 expression peaked, both the level of Atg3 and the number of LC3 puncta per cell (autophagosomes) decreased dramatically. In accordance, miR-155 silencing rescued autophagosome number in Mtb infected DC and enhanced autolysosome fusion, thereby supporting a previously unidentified role of the miR-155 as inhibitor of ATG3 expression. Taken together, our findings suggest how Mtb can manipulate cellular miRNA expression to regulate Atg3 for its own survival, and highlight the importance to develop novel therapeutic strategies against tuberculosis that would boost autophagy.
Computer-Assisted Analysis of 4D Cardiac MR Image Sequences after Myocardial Infarction

Summary Objectives: Spatial-temporal MR image sequences of the heart contain information about shape and motion changes and pathological structures after myocardial infarction. In this paper a Heart Analysis Tool (HeAT) for the quantitative analysis of 4D MR image sequences of infarct patients is presented. Methods: HeAT supports interactive segmentation of anatomical and pathological structures. Registration of Cine- and DE-MR image data is applied to enable their combined evaluation during the analysis process. Partitioning of the myocardium in segments enables the analysis with high local resolution. Corresponding segments are generated and used for inter/intra-patient comparison. Quantitative parameters were extracted and visualized. Results: Parameters like endocard movement in the infarcted area of six infarct patients were computed in HeAT. Parameters in the infarct area show the expected dysfunctional characteristics. Based on theses parameters passive endocardial movement and myocardial areas with decreased contraction could be identified. Conclusion: In contrast to other software tools HeAT supports the combination of contour information of Cine-MR and DE-MR, local analysis with high resolution and inter/intra patient comparison. HeAT enables an observer-independent evaluation of the complex cardiac image data. Using HeAT in further studies can increase the understanding of left ventricle(LV) remodeling.
Pectin Lyase Activity in a Penicillium italicum Strain

An extracellular pectin lyase (PNL) [poly-(methoxygalacturonide)lyase; EC 4.2. 2.10] produced by Penicillium italicum CECT 2294 grown on a surface bran (natural medium) or in a submerged (synthetic medium) culture was investigated. Both culture filtrates showed macerating activity at low pH on cucumber, potato, and orange tissues. The physicochemical properties of the enzyme obtained from both culture methods were identical, as well as its catalytic properties, which were assayed by different methods. The molecular mass of the PNL obtained by gel filtration chromatography was 22 kDa; the isoelectric point was 8.6, as determined by chromatofocusing; and the enzyme was able to catalyze the eliminative cleavage of pectins with low (37%) and high (from 54 to 82%) degrees of esterification. The PNL produced in liquid medium showed a Km for pectin (degree of esterification, 70%) of 3.2 mg/ml, and the optimum pH was 6.0 to 7.0. This enzyme was stable at 50°C and at pH 8.0. The ability of this PNL to macerate plant tissues in acidic environmental conditions, its stability at low pH and temperatures up to 50°C (thus preventing mesophilic microbial growth), and the absence of pectinesterase make this preparation useful for the food industry.