Miracle-dz/UniFAR-FTUs huggingface dataset:
Graphical model selection for Gaussian conditional random fields in the presence of latent variables : theory and application to genetics

The task of performing graphical model selection arises in many applications in science and engineering. The field of application of interest in this thesis relates to the needs of datasets that include genetic and multivariate phenotypic data. There are several factors that make this problem particularly challenging: some of the relevant variables might not be observed, high-dimensionality might cause identifiability issues and, finally, it might be preferable to learn the model over a subset of the collection while conditioning on the rest of the variables, e.g. genetic variants. We suggest addressing these problems by learning a conditional Gaussian graphical model, while accounting for latent variables. Building on recent advances in this field, we decompose the parameters of a conditional Markov random field into the sum of a sparse and a low-rank matrix. We derive convergence bounds for this novel estimator, show that it is well-behaved in the high-dimensional regime and describe algorithms that can be used when the number of variables is in the thousands. Through simulations, we illustrate the conditions required for identifiability and show that this approach is consistent in a wider range of settings. In order to show the practical implications of our work, we apply our method to two real datasets and devise a metric that makes use of an independent source of information to assess the biological relevance of the estimates. In our first application, we use the proposed approach to model the levels of 39 metabolic traits conditional on hundreds of genetic variants, in two independent cohorts. We find our results to be better replicated across cohorts than the ones obtained with other methods. In our second application, we look at a high-dimensional gene expression dataset. We find that our method is capable of retrieving as many biologically relevant gene-gene interactions as other methods while retrieving fewer irrelevant interaction.
The “ Privatization ” of Municipal Debt

State and local governments in the U.S. have substantially increased their reliance on private bank loans in the aftermath of the Great Recession. Using loan-level data on bank lending to U.S. municipal governments, we document that these loans have high effective debt priority and are likely to allow borrowers additional debt capacity. Specifically, banks loans to municipalities are highly collateralized, include additional seniority and guarantee provisions, and have short maturities. Consistent with the idea that financially weak borrowers are more likely to resort to higher priority debt, banks' assessments indicate a non-trivial fraction of municipal borrowers to be high risk. Last, we show that exogenous adverse income shocks lead to a significant increase in bank financing in the debt structure of municipalities. These results suggest that the reliance of municipalities on private debt is likely to increase in an environment of eroding fiscal positions. A version of this paper was presented at the 7th Municipal Finance Conference at The Brookings Institution on July 16-17, 2018. The views stated herein are those of the authors and are not necessarily the views of the Federal Reserve Board or the Federal Reserve System. The authors thank Mitchell Berlin, Ronel Elul, Kathleen Johnson, Byron Lutz, Greg Nini, Robert Sarama, Edison Yu, and seminar participants at the Federal Reserve Board, the Federal Reserve Bank of Philadelphia, and the 2018 Chicago Institutions Conference for helpful comments. They thank Stephen Paolillo for excellent research assistance. The authors did not receive financial support from any firm or person with a financial or political interest in this article. Neither is currently an officer, director, or board member of any organization with an interest in this article.
Caractérisation de panaches industriels par imagerie hyperspectrale

Les capteurs hyperspectraux, qui acquierent des images dans le domaine reflectif ([0,4-2,5µm]), avec une haute resolution spatiale (quelques metres) et dans de nombreuses bandes spectrales simultanement, permettent d’estimer a la fois les proprietes des aerosols atmospheriques et de certains gaz. Les travaux presentes ici portent sur la caracterisation de panaches industriels. Les particules emises par les industries ont des proprietes encore tres mal connues et les bases de donnees actuelles ne contiennent pas les informations necessaires a la comprehension et la modelisation de leur impact radiatif. La premiere partie de cette etude consiste donc a caracteriser les proprietes physiques et optiques de ces aerosols, a partir d’echantillons preleves, et a conduit a l’etablissement d’un modele permettant de decrire l’impact radiatif d’un panache emis par une industrie metallurgique. Dans une seconde partie, une methode d’estimation conjointe du CO2 et des aerosols est proposee. Il a ete montre, a partir d’une etude de sensibilite et de l’application de cette methode sur deux images AVIRIS, que cette estimation conjointe, dans le cas des panaches optiquement denses, conduisait a une erreur d’estimation du CO2 divisee d’un facteur 2 par rapport aux techniques existantes (e. G. JRGE). Enfin, une methode d’estimation du type d’aerosols, EARTH (Estimation of Aerosol Type using Hyperspectral data), specifiquement adaptee aux panaches industriels, a ete developpee. Une validation sur donnees simulees et reelles (image CASI) a montre qu’elle permettait de reconnaitre, sans information a priori, la presence de particules metalliques dans un panache de faible epaisseur optique.
Acetaminophen as a Renoprotective Adjunctive Treatment in Patients With Severe and Moderately Severe Falciparum Malaria : A Randomized , Controlled , Open-Label Trial

Author(s) Plewes, Katherine; Kingston, Hugh W. F. ; Ghose, Aniruddha; Wattanakul, Thanaporn; Md. Mahtab Uddin Hassan; Md. Shafiul Haider; Dutta, Prodip K. ; Md. Akhterul Islam; Shamsul Alam; Selim Md. Jahangir; Zahed, A. S. M. ; Md. Abdus Sattar; Chowdhury, M. A. Hassan; Herdman, M. Trent; Leopold, Haruhiko; Piera, Kim A; Charunwatthana, Prakaykaew; Silamut, Kamolrat; Yeo, Tsin Wen; Lee, Sue J.; Mukaka, Mavuto; Maude, Richard J.; Turner, Gareth D. H. ; Md. Abul Faiz; Tarning, Joel; Oates, John A. ; Anstey, Nicholas M. ; White, Nicholas J.; Day, Nicholas P. J.; Md. Amir Hossain; Roberts II, L. Jackson; Dondorp, Arjen M.
Laparoscopic distal pancreatectomy: feasibility study of radiofrequency-assisted transection in a porcine model.

BACKGROUND AND AIM Despite technological improvements in pancreatic surgery, the incidence and morbidity of pancreatic leak after resection of distal pancreas are persistently high in most series. Laparoscopic distal pancreatectomy (LDP) is today the gold standard procedure for benign and certain malignant neoplasms of the pancreatic body and tail in specialized centers. This study evaluated safety and feasibility of a radiofrequency (RF)-assisted transection device in a porcine model of LDP. MATERIALS AND METHODS LDP was performed on 10 pigs (median weight, 39.6 kg) using a new device based on an internally cooled RF-assisted electrode (Coolinside(®), Apeiron Medical, Valencia, Spain). The animals were subjected to daily observation and then sacrificed and necropsied at 4 weeks postoperatively. Primary end points were the development of postoperative pancreatic fistula using the Pancreatic Anastomotic Leak Study Group definition and/or the presence of abdominal amylase-rich fluid collections or abscesses during necropsy and pathological study and/or dye extravasation from the pancreatic remnant duct. Secondary end points were intra- or postoperative complications, surgery, and transection duration. RESULTS No clinically relevant postoperative pancreatic fistulas were observed. In one case a grade A postoperative fistula was diagnosed due to amylase drain concentration of more than 6200 IU/mL on postoperative day 4. Median peritoneal liquid amylase concentration on postoperative day 4 was 2399.0 IU/L (range, 819.2-7122.0 IU/L), similar to the median plasma amylase level of 1520.8 IU/L (range, 1015.3-4056.6 IU/L). Median surgery time was 93.5 minutes (range, 46.0-140.0 minutes), and median transection time was 4.5 minutes (range, 2.0-26.0 minutes). There was one postoperative wound infection. There were no postoperative deaths or major complications. During the histopathological study, the surgical margin of the remaining pancreas showed a common pattern with a central area of necrosis surrounded by granulomatous infiltrate and fibrosis. Ductal obliteration was observed. No purulent inflammatory infiltrate or abscesses were present. CONCLUSION Experimental findings suggest that performing pancreatic transection with Coolinside in a animal model of LDP is feasible and safe.
Analyzing time evolution of constraint equations of Einstein's equation

We propose a method of analyzing the time evolution of constraint equations of the Einstein’s equation on the nonflat background by adding constraint terms to the evolution equations. In past studies, the eigenvalues of the coefficient matrix of the constraint equations was mostly obtained on the flat background. Since simulations do not always perform near the flat background, we need to calculate the eigenvalues on the appropriate background. We analyze eigenvalues numerically and predict the stability in the appropriate background. We also perform some numerical simulations and show consistency between the results of the eigenvalue analysis and the numerical stability.
The Effect of Crystal Size and Dispersed-Solid Inclusions on the Activation Energy for Creep of Ice

Abstract Steady-state creep-rates of polycrystalline ice were investigated as a function of temperature, grain-size, and inclusion concentration through uniaxial compression in the laboratory. Samples were run at a constant load with the temperature systematically varied between about —5°C and —40°C. The presence of inclusions inhibits dynamic recrystallization and grain growth; the average crystal size produced by recrystallization is inversely proportional to the inclusion concentration. At temperatures above —8°C, creep-rate is enhanced by about a factor of two. This appears to be the result of the combined effects of recrystallization with accompanying grain growth and grain-boundary sliding. Over the temperature range —10°C to —40°C, the apparent activation energy for creep increases with increasing volume fraction of inclusions. This is apparently due to a thermally activated process which is modified by internal stresses created by the inclusions.
A Comprehensive Technological Survey on the 2 Dependable Self-management CPS : from 3 self-adaptive architecture to self-management 4 strategies 5

Cyber Physical Systems (CPS) has been a popular research area in the last decade. The 17 dependability of CPS is still a critical issue, and rare survey has been published in this domain. CPS 18 is a dynamic complex system, which involves various multidisciplinary technologies. To avoid 19 human error and to simplify management, self-management CPS (SCPS) is a wise choice. And to 20 achieve dependable self-management, systematic solution is necessary to verify the design and to 21 guarantee the safety of self-adaptation decision, as well as to maintain the health of SCPS. This 22 survey first recalls the concepts of dependability, and proposes a generic environment-in-loop 23 processing flow of self-management CPS, and then analyzes the error sources and challenges of 24 self-management through the formal feedback flow. Focus on reducing the complexity, we first 25 survey the self-adaptive architecture approaches and applied dependability means; then we 26 introduce a hybrid multi-role self-adaptive architecture, and discuss the supporting technologies 27 for dependable self-management at the architecture level. Focus on dependable 28 environment-centered adaption, we investigate the verification and validation (V&V) methods for 29 making safe self-adaptation decision and the solutions for processing decision dependably. For 30 system-centered adaption, the comprehensive self-healing methods are summarized. Finally, we 31 analyze the missing pieces of the technology puzzle and the future directions. In this survey, the 32 technical trends for dependable CPS design and maintenance are discussed, an all-in-one solution 33 is proposed to integrate these technologies and build a dependable organic SCPS. To the best of our 34 knowledge, this is the first comprehensive survey on dependable SCPS building and evaluation. 35
effectiveness of the “elderly Activity Performance Intervention” on elderly patients’ discharge from a short-stay unit at the emergency department: a quasi-experimental trial

Purpose: To examine the effectiveness of the Elderly Activity Performance Intervention on reducing the risk of readmission in elderly patients discharged from a short-stay unit at the emergency department. Patients and methods: The study was conducted as a nonrandomized, quasi-experimental trial. Three hundred and seventy-five elderly patients were included and allocated to the Elderly Activity Performance Intervention (n = 144) or usual practice (n = 231). The intervention consisted of 1) assessment of the patients’ performance of daily activities, 2) referral to further rehabilitation, and 3) follow-up visit the day after discharge. Primary outcome was readmission (yes/no) within 26 weeks. The study was registered in ClinicalTrial.gov (NCT02078466). Results: No between-group differences were found in readmission. Overall, 44% of the patients in the intervention group and 42% in the usual practice group were readmitted within 26 weeks (risk difference = 0.02, 95% CI: [ − 0.08; 0.12] and risk ratio = 1.05, 95% CI: [0.83; 1.33]). No between-group differences were found in any of the secondary outcomes. Conclusion: The Elderly Activity Performance Intervention showed no effectiveness in reducing the risk of readmission in elderly patients discharged from a short-stay unit at the emergency department. The study revealed that 60% of the elderly patients had a need for further rehabilitation after discharge.
Serveur Académique Lausannois SERVAL serval.unil.ch

Astrocytes are the most abundant glial cell type in the brain. Although not apposite for long-range rapid electrical communication, astrocytes share with neurons the capacity of chemical signaling via Ca 2+ -dependent transmitter exocytosis. Despite this recent finding, little is known about the specific properties of regulated secretion and vesicle recycling in astrocytes. Important differences may exist with the neuronal exocytosis, starting from the fact that stimulus-secretion coupling in astrocytes is voltage independent, mediated by G-protein-coupled receptors and the release of Ca 2+ from internal stores. Elucidating the spatiotemporal properties of astrocytic exo-endocytosis is, therefore, of primary importance for understanding the mode of communication of these cells and their role in brain signaling. We here take advantage of fluorescent tools recently developed for studying recycling of glutamatergic vesicles at synapses (Voglmaier et al., 2006; Balaji and Ryan, 2007); we combine epifluorescence and total internal reflection fluorescence imaging to investigate with unprecedented temporal and spatial resolution, the stimulus-secretion coupling underlying exo-endocytosis of glutamatergic synaptic-like microvesicles (SLMVs) in astrocytes. Our main findings indicate that (1) exo-endocytosis in astrocytes proceeds with a time course on the millisecond time scale ( τ exocytosis = 0.24 ± 0.017 s; τ endocytosis = 0.26 ± 0.03 s) and (2) exocytosis is controlled by local Ca 2+ microdomains. We identified submicrometer cytosolic compartments delimited by endoplasmic reticulum tubuli reaching beneath the plasma membrane and containing SLMVs at which fast (time-to-peak, ∼ 50 ms) Ca 2+ events occurred in precise spatial-temporal correlation with exocytic fusion events. Overall, the above characteristics of transmitter exocytosis from astrocytes support a role of this process in fast synaptic modulation.
Molecular basis for the function of the (cid:2)(cid:3) heterodimer of human NAD-dependent isocitrate dehydrogenase

Mammalian mitochondrial NAD-dependent isocitrate dehydrogenase (NAD-IDH) catalyzes the decarboxylation of isoci-trateinto (cid:2) -ketoglutarateinthetricarboxylicacidcycle.Itexists as the (cid:2) 2 (cid:3)(cid:4) heterotetramer composed of the (cid:2)(cid:3) and (cid:2)(cid:4) heterodimers. Different from the (cid:2)(cid:4) heterodimer that can be allosterically activated by CIT and ADP, the (cid:2)(cid:3) heterodimer cannot be allosterically regulated by the activators; however, the molecular mechanism is unclear. We report here the crystal structures of the (cid:2)(cid:3) heterodimer of human NAD-IDH with the (cid:2) subunit in apo form and in Ca 2 (cid:5) -bound, NAD-bound, and NADH-bound forms. Structural analyses and comparisons reveal that the (cid:2)(cid:3) heterodimer has a similar yet more compact overall structure compared with the (cid:2)(cid:4) heterodimer and contains a pseudo-allosteric site that is structurally different from the allosteric site.
Sugar-sweetened beverage consumption and incident hypertension : a systematic review and meta-analysis of prospective cohorts 1 – 3

Background: The role of sugar-sweetened beverages (SSBs) that contain free or bound fructose in the pathogenesis of hypertension remains unclear. Objective: We conducted a systematic review and meta-analysis of prospective cohort studies to quantify the association between fructose-containing SSBs and risk of hypertension. Design: MEDLINE, Embase, Cumulative Index to Nursing and Allied Health Literature, and the Cochrane registry were searched from conception through 11 November 2014. Two independent reviewers extracted data and assessed the quality of studies (with the use of the Newcastle-Ottawa Scale). Risk estimates of extreme quantiles of SSB intake (lowest vs. highest) for hypertension incidence were generated with the use of generic inverse-variance methods with random-effects models and expressed as risk ratios with 95% CIs. Heterogeneity was assessed with the Cochran Q statistic and quantified with the I statistic. Results: Six prospective cohort studies (n = 240,508) with 79,251 cases of hypertension observed over $3,197,528 person-years of follow-up were included. SSB consumption significantly increased the risk of developing hypertension by 12% (risk ratio: 1.12; 95% CI: 1.06, 1.17) with evidence of significant heterogeneity (I = 62%, P = 0.02) when highest ($1-serving [6.7, 8 or 12 oz]/d) and lowest (none) quantiles of intake were compared. With the use of a dose-response analysis, a significant 8.2% increase in risk of every additional SSB per day from none to $1 SSB/d (b = 0.0027, P , 0.001) was identified. Limitations include unexplained heterogeneity and residual confounding. The results may also have been subject to collinearity effects from aspects of a Western dietary pattern. Conclusions: SSBs were associated with a modest risk of developing hypertension in 6 cohorts. There is a need for high-quality randomized trials to assess the role of SSBs in the development of hypertension and its complications. This study was registered at clinicaltrials.gov as NCT01608620. Am J Clin Nutr doi: 10.3945/ajcn.115. 107243.
Development of RAMS-CMAQ to Simulate Aerosol Optical Depth and Aerosol Direct Radiative Forcing and Its Application to East Asia

Abstract The air quality modeling system RAMS (Regional Atmospheric Modeling System)-CMAQ (Models-3 Community Multi—scale Air Quality) is developed to simulate the aerosol optical depth (AOD) and aerosol direct forcing (DF). The aerosol—specific extinction, single scattering albedo, and asymmetry factor are parameterized based on Mie theory taking into account the aerosol size distribution, composition, refractive index, and water uptake of solution particles. A two—stream solar radiative model considers all gaseous molecular absorption, Rayleigh scattering, and aerosols and clouds. RAMS—CMAQ is applied to simulate all major aerosol concentrations (e.g., sulfate, nitrate, ammonium, organic carbon, black carbon, fine soil, and sea salt) and AOD and DF over East Asia in 2005. To evaluate its performance, the simulated AOD values were compared with ground—based in situ measurements. The comparison shows that RAMSCMAQ performed well in most of the model domain and generally captured the observed variations. High AOD values (0.2—1.0) mainly appear in the Sichuan Basin as well as in central and southeastern China. The geographic distribution of DF generally follows the AOD distribution patterns, and the DF at the top-of-the-atmosphere is less than –25 and –20 W m-2 in clear-sky and all-sky over the Sichuan Basin. Both AOD and DF exhibit seasonal variations with lower values in July and higher ones in January. The DF could obviously be impacted by high cloud fractions.
Clinical Findings for a Group 01 Children with Auditory

Objective: To examine the prevalence of auditory neuropathy in a group of infants at risk for hearing impairment and to present an overview of the clin ical findings for affected children. Design: Results for 20 subjects who showed repeat able cochlear microphonic potentials in the absence of click-evoked auditory brain stem responses are included in this study. Behavioral and steady state evoked potential thresholds were established in each case. Where possible, otoacoustic emission and speech perception results (unaided and aided) also were obtained. Results: One in 433 (0.23"/() of the children in our series had evidence of auditory neuropathy. The audiometric findings for these subjects varied sig nificantly, with behavioral thresholds ranging from normal to profound levels. Discrimination skills were also variable. Approximately half of the sub jects showed little understanding, or even aware ness, ofspeech inputs in both the unaided and aided conditions. There were, however, a number of chil dren who could score at significant levels on speech discrimination tasks and who benefited from the provision of amplification. Conclusion: The results suggest that auditory neu ropathy is more common in the infant population than previously suspected. The effects of neuropa thy on auditory function appear to be idiosyncratic, producing significant variations in both the detec tion and discrimination of auditory signals. As such, the management of children with this disorder must allow for individual differences.
My Lips : Speech distortions in musical lyrics can be overcome ( slightly ) by facial information

Understanding the lyrics of many contemporary songs is difficult, and an earlier study (Hidalgo-Barnes and Massaro, 2007) showed a benefit for lyrics recognition when seeing a computer-animated talking head (Baldi®), mouthing the lyrics along with hearing the singer. However, the contribution of visual information was relatively small compared to what is usually found for speech. In the current experiments, our goal was to determine why the face appears to contribute less when aligned with sung lyrics than when aligned with normal speech presented in noise. The first experiment compared the contribution of the talking head with the originally-sung lyrics versus the case when it was aligned with the Festival TtS spoken at the original duration of the song’s lyrics. A small and similar influence of the face was found in both conditions. In the next three experiments, we compared the presence of the face when the durations of the TtS were equated with the duration of the original musical lyrics to the case when the lyrics were read with typical TtS durations and this speech embedded in noise. The results indicated that the unusual temporally-distorted durations of musical lyrics decreases the contribution of the visible speech from the face.