Miracle-dz/UniFAR-FTUs huggingface dataset:
The Flexible Cubic Polynomial and Plateau Production Functions

The S-shaped three-stage production function, popular in teaching economics and farm management, is often motivated in the context of yield response to fertilization and illustrated using a third degree polynomial specification (cubic). Indeed, the cubic model is used as basis for fertilization recommendations and norm setting in Denmark. Yet, contemporary agricultural economic and agronomic knowledge favors non-linear response with plateau (NLRP) specifications. An analysis, based on fitting the cubic to yield/nitrogen data sets from 40 Danish winter wheat field trials, did not in a single case reveal a three-stage response pattern. It is interesting, however, that in the majority of 40 estimations, the cubic exhibited or strongly suggested an NLRP-like pattern within the domain of measured nitrogen application. Thus, the flexible cubic often works well for the purpose of norm setting when care is taken to avoid extrapolation outside the data domain. *Bruce R. Beattie is Professor and Jorgen R. Mortensen is Bartley P. Cardon Research Specialist in the Department of Agricultural and Resource Economics, University of Arizona, Tucson 85721-0023. Leif Knudsen is Plant Nutrition Chief Adviser, Danish Agricultural Advisory Service, Skejby, Denmark
Inhibition of C3 Convertase Activity by Hepatitis C Virus as an Additional Lesion in the Regulation of Complement Components

We have previously reported that in vitro HCV infection of cells of hepatocyte origin attenuates complement system at multiple steps, and attenuation also occurs in chronically HCV infected liver, irrespective of the disease stage. However, none of these regulations alone completely impaired complement pathways. Modulation of the upstream proteins involved in proteolytic processing of the complement cascade prior to convertase formation is critical in promoting the function of the complement system in response to infection. Here, we examined the regulation of C2 complement expression in hepatoma cells infected in vitro with cell culture grown virus, and validated our observations using randomly selected chronically HCV infected patient liver biopsy specimens. C2 mRNA expression was significantly inhibited, and classical C3 convertase (C4b2a) decreased. In separate experiments for C3 convertase function, C3b deposition onto bacterial membrane was reduced using HCV infected patient sera as compared to uninfected control, suggesting impaired C3 convertase. Further, iC3b level, a proteolytically inactive form of C3b, was lower in HCV infected patient sera, reflecting impairment of both C3 convertase and Factor I activity. The expression level of Factor I was significantly reduced in HCV infected liver biopsy specimens, while Factor H level remained unchanged or enhanced. Together, these results suggested that inhibition of C3 convertase activity is an additional cumulative effect for attenuation of complement system adopted by HCV for weakening innate immune response.
Conjugated linoleic acid improves glycemic response, lipid profile, and oxidative stress in obese patients with non-alcoholic fatty liver disease: a randomized controlled clinical trial

Aim To investigate if conjugated linoleic acid supplementation (CLA) affects metabolic factors and oxidative stress in non-alcoholic fatty liver disease (NAFLD). Methods The study was a randomized, controlled clinical trial conducted in specialized and subspecialized clinics of Tabriz University of Medical Sciences from January 2014 to March 2015. 38 obese NAFLD patients were randomly allocated into either the intervention group, receiving three 1000 mg softgel of CLA with a weight loss diet and 400 IU vitamin E, or into the control group, receiving only weight loss diet and 400 IU vitamin E for eight weeks. Dietary data and physical activity, as well as anthropometric, body composition, metabolic factors, and oxidative stress were assessed at baseline and at the end of the study. Results Weight, body composition, and serum oxidative stress, insulin, and lipid profile significantly improved in both groups, while hemoglobin A1c (HbA1c) levels (P = 0.004), total cholesterol to high density lipoprotein ratio (P = 0.008), low density lipoprotein to high density lipoprotein ratio (LDL/HDL) (P = 0.002), and alanine aminotransferase to aspartate aminotransferase (ALT/AST) ratio (P = 0.025) significantly decreased in the intervention group. At the end of the study, fat mass (P = 0.001), muscle mass (P = 0.023), total body water (P = 0.004), HbA1c (P < 0.001), triglycerides (P = 0.006), LDL/HDL ratio (P = 0.027), and ALT/AST ratio (P = 0.046) were significantly better in the CLA group than in the control group. Conclusion CLA improved insulin resistance, lipid disturbances, oxidative stress, and liver function in NAFLD. Therefore, it could be considered as an effective complementary treatment in NAFLD. Registration number: IRCT2014020516491N1.
USER-CENTRIC EVALUATION OF DIGITAL LIBRARIES: THREE CASE STUDIES

Cultural heritage digital libraries have a range of users including professionals; "digital natives" as well as general users. Their motivation and needs differ and one of the challenges in evaluating how digital libraries are perceived is to understand the specific points of view of various communities. The identification of stumbling blocks and features which are not satisfying users' expectations is aimed not only to develop a clearer understanding of users and to serve them better but also to sustain a steady user community. The paper addresses how user evaluations could help to adapt the digital libraries to the users. Three case studies will illustrate how a range of user communities within the art and cultural heritage domain were studied. The first one treats the user survey initiative held for the Italian Association of Librarians AIB portal, launched in the phase of its re-styling through a web questionnaire that collected more than 600 answers. The second, within the project DiSCmap, studied the needs in digitized materials within the Higher Education institutions in the UK. The third one assessed the European digital library Europeana through a combination of focus groups and media labs held in four countries. This study was qualitative but gathered a range of quantitative data providing evidence of user behaviour (queries used; eye tracking data and data on the users' performance on a standard set of tasks). All those studies synthesized recommendations on the preferred characteristics and features of the digital libraries from the point of view of specific user communities. The paper will provide practical examples which illustrate how quantitative and qualitative elements in a user study help to build a better picture of the users' needs.
Cancer risk in the Swiss HIV Cohort Study: associations with immunodeficiency, smoking, and highly active antiretroviral therapy.

BACKGROUND Persons infected with human immunodeficiency virus (HIV) have an increased risk for several cancers, but the influences of behavioral risk factors, such as smoking and intravenous drug use, and highly active antiretroviral therapy (HAART) on cancer risk are not clear. METHODS Patient records were linked between the Swiss HIV Cohort Study and Swiss cantonal cancer registries. Observed and expected numbers of incident cancers were assessed in 7304 persons infected with HIV followed for 28,836 person-years. Relative risks for cancer compared with those for the general population were determined by estimating cancer registry-, sex-, age-, and period-standardized incidence ratios (SIRs). RESULTS Highly elevated SIRs were confirmed in persons infected with HIV for Kaposi sarcoma (KS) (SIR = 192, 95% confidence interval [CI] = 170 to 217) and non-Hodgkin lymphoma (SIR = 76.4, 95% CI = 66.5 to 87.4). Statistically significantly elevated SIRs were also observed for anal cancer (SIR = 33.4, 95% CI = 10.5 to 78.6); Hodgkin lymphoma (SIR = 17.3, 95% CI = 10.2 to 27.4); cancers of the cervix (SIR = 8.0, 95% CI = 2.9 to 17.4); liver (SIR = 7.0, 95% CI = 2.2 to 16.5); lip, mouth, and pharynx (SIR = 4.1, 95% CI = 2.1 to 7.4); trachea, lung, and bronchus (SIR = 3.2, 95% CI = 1.7 to 5.4); and skin, nonmelanomatous (SIR = 3.2, 95% CI = 2.2 to 4.5). In HAART users, SIRs for KS (SIR = 25.3, 95% CI = 10.8 to 50.1) and non-Hodgkin lymphoma (SIR = 24.2, 95% CI = 15.0 to 37.1) were lower than those for nonusers (KS SIR = 239, 95% CI = 211 to 270; non-Hodgkin lymphoma SIR = 99.3, 95% CI = 85.8 to 114). Among HAART users, however, the SIR (although not absolute numbers) for Hodgkin lymphoma (SIR = 36.2, 95% CI = 16.4 to 68.9) was comparable to that for KS and non-Hodgkin lymphoma. No clear impact of HAART on SIRs emerged for cervical cancer or non-acquired immunodeficiency syndrome-defining cancers. Cancers of the lung, lip, mouth, or pharynx were not observed among nonsmokers. CONCLUSION In persons infected with HIV, HAART use may prevent most excess risk of KS and non-Hodgkin lymphoma, but not that of Hodgkin lymphoma and other non-acquired immunodeficiency syndrome-defining cancers. No cancers of the lip, mouth, pharynx, or lung were observed in nonsmokers.
Inverse Reinforcement Learning algorithms and features for robot navigation in crowds: An experimental comparison

For mobile robots which operate in human populated environments, modeling social interactions is key to understand and reproduce people's behavior. A promising approach to this end is Inverse Reinforcement Learning (IRL) as it allows to model the factors that motivate people's actions instead of the actions themselves. A crucial design choice in IRL is the selection of features that encode the agent's context. In related work, features are typically chosen ad hoc without systematic evaluation of the alternatives and their actual impact on the robot's task. In this paper, we introduce a new software framework to systematically investigate the effect features and learning algorithms used in the literature. We also present results for the task of socially compliant robot navigation in crowds, evaluating two different IRL approaches and several feature sets in large-scale simulations. The results are benchmarked according to a proposed set of objective and subjective performance metrics.
Considerations and complications of mapping small RNA libraries to transposable elements

The advent of high-throughput sequencing (HTS) has revolutionized the way in which epigenetic research is conducted. Often coupled with the availability of fully sequenced genomes, millions of small RNA (sRNA) reads are mapped to regions of interest and the results scrutinized for clues about epigenetic mechanisms. However, this approach requires careful consideration in regards to experimental design, especially when one investigates repetitive parts of genomes such as transposable elements (TEs), and especially when such genomes are large as is often the case in plants. Here, to shed light on the challenges of mapping sRNAs to TEs, we focus on the 2,300Mb maize genome, of which >85% is derived from TEs. We compare various methodological strategies that are commonly employed in TE studies. These include choices for the reference dataset, the normalization of multiple mapping sRNAs, and the selection among different types of sRNA metrics. We further examine how these choices influence the relationship between sRNAs and the critical feature of TE age, and explore and contrast their effect on low copy regions (exons) and other popular HTS data (RNA-seq). Finally, based on our analysis, we share a series of take-home messages to help guide TE epigenetic studies specifically, but our conclusions may also apply to any work that involves mapping and analysis of HTS data.
Striking Divergence in Toxoplasma ROP16 Nucleotide Sequences From Human and Meat Samples.

BACKGROUND ROP16 is a protein kinase of Toxoplasma gondii identified in the mouse model as a virulent marker, but it is unknown whether this finding is relevant in human toxoplasmosis. METHODS We obtained the Toxoplasma ROP16 locus DNA sequence in samples from 12 patients with ocular toxoplasmosis, 1 sample from a patient with congenital toxoplasmosis, 22 samples from soldiers operating in the jungle, 2 samples from urban soldiers, and 10 samples from meat for human consumption. An enzyme-linked immunosorbent assay specific for antibodies against the ROP16 mouse-virulent peptide was performed in 46 serum specimens from patients with ocular toxoplasmosis and in 28 serum specimens from patients with chronic asymptomatic infection, of whom 19 had congenital infection and 11 had toxoplasmic lymphadenitis. RESULTS We found a striking divergence of the ROP16 nucleotide sequences. Ten of 12 sequences (83.3%) from patients with ocular toxoplasmosis clustered with those of mouse-virulent strains, whereas 7 of 7 ROP16 sequences (100%) from meat were clustered with those of mouse-avirulent strains. Only 11 of 104 serum specimens (10.5%) had specific antibodies against the mouse-virulent peptide, and there was no association between clinical forms and positive results of serological assays. CONCLUSIONS The majority of ROP16 nucleotide sequences from Colombian patients with ocular toxoplasmosis belonged to the group of mouse-virulent strains.
Protein Aggregation after Transient Cerebral Ischemia

Protein aggregates containing ubiquitinated proteins are commonly present in neurodegenerative disorders and have been considered to cause neuronal degeneration. Here, we report that transient cerebral ischemia caused severe protein aggregation in hippocampal CA1 neurons. By using ethanolic phosphotungstic acid electron microscopy (EM) and ubiquitin immunogold EM, we found that protein aggregates were accumulated in CA1 neurons destined to die 72 hr after 15 min of cerebral ischemia. Protein aggregates appeared as clumps of electron-dense materials that stained heavily for ubiquitin and were associated with various intracellular membranous structures. The protein aggregates appeared at 4 hr and progressively accumulated at 24 and 48 hr of reperfusion in CA1 dying neurons. However, they were rarely observed in dentate gyrus neurons that were resistant to ischemia. At 4 hr of reperfusion, protein aggregates were mainly associated with intracellular vesicles in the soma and dendrites, and the nuclear membrane. By 24 hr of reperfusion, the aggregates were also associated with mitochondria, the Golgi apparatus, and the dendritic plasmalemma. High-resolution confocal microscopy further demonstrated that protein aggregates containing ubiquitin were persistently and progressively accumulated in all CA1 dying neurons but not in neuronal populations that survive in this model. We conclude that proteins are severely aggregated in hippocampal neurons vulnerable to transient brain ischemia. We hypothesize that the accumulation of protein aggregates cause ischemic neuronal death.
Mentalizing in Organizations: A Psychodynamic Model for an Understanding of Well-Being and Suffering in the Work Contexts

Moving from the paradigms of “mentalization” and “reflective function” (Fonagy and colleagues), this article develops the concept of “mentalizing” in organizations, understood as a process of construction of shared meaning in the work contexts, and whose absence or deterioration produces suffering in organizational experience, exposing individuals to significant psychosocial risks. This model converges in outlining a framework in which the absence of a reflective competence and the lack of symbolization of the experience of work fall on the perception of one's own job, and on the relationship with colleagues and management, producing unsustainability of the work experience. The availability of reflective spaces that are inscribed in the ordinary dimension of work thus appears as a solution capable of promoting organizational well-being.
Quantitative Games on Probabilistic Timed Automata

Two-player zero-sum games are a well-established model for synthesising controllers that optimise some performance criterion. In such games one player represents the controller, while the other describes the (adversarial) environment, and controller synthesis corresponds to computing the optimal strategies of the controller for a given criterion. Asarin and Maler initiated the study of quantitative games on (non-probabilistic) timed automata by synthesising controllers which optimise the time to reach a final state. The correctness and termination of their approach was dependent on exploiting the properties of a special class of functions, called simple functions, that can be finitely represented. In this paper we consider quantitative games over probabilistic timed automata. Since the concept of simple functions is not sufficient to solve games in this setting, we generalise simple functions to so-called quasi-simple functions. Then, using this class of functions, we demonstrate that the problem of solving games with either expected reachability-time or expected discounted-time criteria on probabilistic timed automata are in NEXPTIME $\cap$ co-NEXPTIME.
Terminal The Architecture of the Active Zone in the Presynaptic Nerve

http://www.the-aps.org/. Pike, Bethesda MD 20814-3991. © 2004 Int. Union Physiol. Sci./Am. Physiol. Soc. ESSN: 1548-9221. Visit our website at is published bimonthly in February, April, June, August, October, and December by the American Physiological Society, 9650 Rockville (formerly published as News in Physiological Science) publishes brief review articles on major physiological developments. It Physiology by gest on O cber 9, 2016 http://physioline.physiology. org/ D ow nladed fom
A Critique of Intensive Courses and an Agenda for Research.

Voluntary freshman attritition and patterns of social and academic integration in a university: A test of a conceptual model. The relation of students' precollege experiences and freshman year experience to voluntary attrition. (1967). Estimation of the probability of an event as a function of several independent variables. Biometrika 54: 167-179. White, K.J. (1987). SHAZAM: A general computer program for econometric methods. (1976). Regression with qualitative and quantitative variables: An alternating least squares algorithm with optimal scaling features. Traditional course formats have remained relatively unchanged in American higher education: most colleges and universities schedule their courses several times per week for 12 to 16 weeks. Although there has been little evidence to support their use over various alternatives, traditional course formats continue to dominate in higher education owing to long-standing collegiate and bureaucratic traditions (HefferJin, 1972). Recently, however, changing student demographics have prompted a rapidly growing interest in intensive courses-semester-or quarter-equivalent classes offered in compressed formats. Concerned with maintaining enrollments, colleges and universities are courting adult and part-time students by offering intensive courses which better accommodate students' schedules. As a result, thousands of students have been afforded the opportunity to pursue a baccalau-reate or post-baccalaureate degree which otherwise might have been impossible. Yet, the growing presence of intensive courses on many college and university campuses has generated disapproval among many faculty and administrators. Conventional wisdom has long criticized intensive courses as being too compressed "to produce anything of educational value" (Slichter in Schoenfeld, 1967, p. 160). They have been reproached for sacrificing breadth, short-shrifting academic standards to accommodate time constraints, and obliging students to "cram" information at the expense of genuine learning and development. Nevertheless, given adult and part-time student demographic trends, intensive courses probably will proliferate in the future. According to the National Center for Education Statistics (1989a), adult student enrollments increased 114 percent between 1970 and 1985 and now constitute an estimated 42 percent of post
The Effects of CREB-mediated BDNF Expression on Memory- and Anxiety-related Behaviours in the Adult Mouse

Experience drives changes in gene expression that mold and reorganize neuronal circuits. In response to neuronal activity, the transcription factor CREB binds to a regulatory site on Bdnf promoter IV to modulate BDNF protein levels. CREB and BDNF are extensively implicated in animal behaviour, but the role of the interaction between these proteins has not been studied. I used transgenic mice carrying mutations at the CREB binding site of Bdnf promoter IV (CREmKI mutation) to specifically disrupt this interaction. F1 (N = 52) and F2 (N = 69) mice underwent a battery of behavioural tests. All mice showed normal motor learning and spatial memory. Critically, F1 mutants showed impaired auditory fear memory, while F2 mutants showed heightened anxiety. I suspect that differences in Bdnf expression and compensatory effects contributed to discrepancies between the two generations. My findings highlight the relevance of BDNF expression levels for memoryand anxiety-related behaviours.
Warped DFT as the basis for psychoacoustic model

We consider the warped DFT as an alternative basis for psychoacoustic models. The appropriate construction of the transform is approached, aiming for precise critical band power analysis. It is shown that sufficient spectral resolution can be obtained for sample block lengths several times shorter than the 1024 or 2048 commonly used in the FFT based ear models. Thus, temporal resolution is improved and comparable with that of more complex perceptual models utilizing filter banks. The computational complexity is estimated as acceptable for realtime processing.
SUMER observations of Doppler shift in the quiet Sun and in an active region

The UV spectral lines formed at transition region temperatures in the solar atmosphere, show a prevailing red- shifted emission. Using the Solar Ultraviolet Measurements of Emitted Radiation spectrometer flown on the Solar and He- liospheric Observatoryspacecraft, we measure the amount of line shift as a function of the temperature for several spectral lines formed in the range between 10 4 and 10 6 K. We analyze spectrograms relative to the quiet Sun and to the active region NOAA7946. The velocities derived are increasing from a red- shift of � 0k ms 1 at � 20000 Kt o10 km s 1 at 1. 91 0 5 K for the quiet Sun, and to � 15 km s 1 at 10 5 K for the active re- gion. At higher temperature an opposite behaviour is observed. In the quiet Sun a blueshift of � 2k ms 1 is observed at the Neviii formation temperature (6. 31 0 5 K), while in the active region, a blue-shifted value around 8k ms 1 is observed for the same spectral line. The finding of blueshift in Ne viii is due to the adoption of a new rest wavelength of 770.428 ˚ A. By10 6 K the blueshift is � 10 km s 1 in the active region as measured
Online (Budgeted) Social Choice

We consider a classic social choice problem in an online setting. In each round, a decision maker observes a single agent's preferences overa set of $m$ candidates, and must choose whether to irrevocably add a candidate to a selection set of limited cardinality $k$. Each agent's (positional) score depends on the candidates in the set when he arrives, and the decision-maker's goal is to maximize average (over all agents) score. We prove that no algorithm (even randomized) can achieve an approximationfactor better than $O(\frac{\log\log m}{\log m})$. In contrast, if the agents arrive in random order, we present a $(1 - \frac{1}{e} - o(1))$-approximatealgorithm, matching a lower bound for the off-line problem.We show that improved performance is possible for natural input distributionsor scoring rules. Finally, if the algorithm is permitted to revoke decisions at a fixedcost, we apply regret-minimization techniques to achieve approximation $1 - \frac{1}{e} - o(1)$ even for arbitrary inputs.