Miracle-dz/UniFAR-FTUs huggingface dataset:
Is Early Tuberculosis Death Associated with Increased Tuberculosis Transmission?

Introduction Tuberculosis (TB) is now a relatively uncommon disease in high income countries. As such, its diagnosis may be missed or delayed resulting in death before or shortly after the introduction of treatment. Whether early TB death is associated with increased TB transmission is unknown. To determine the transmission risk attributable to early TB death we undertook a case-control study. Methods All adults who were: (1) diagnosed with culture-positive pulmonary TB in the Province of Alberta, Canada between 1996 and 2012, and (2) died a TB-related death before or within the first 60 days of treatment, were identified. For each of these “cases” two sets of “controls” were randomly selected from among culture-positive pulmonary TB cases that survived beyond 60 days of treatment. “Controls” were matched by age, sex, population group, +/- smear status. Secondary cases of “cases” and “controls” were identified using conventional and molecular epidemiologic tools and compared. In addition, new infections were identified and compared in contacts of “cases” that died before treatment and contacts of their smear-matched “controls”. Conditional logistic regression was used to find associations in both univariate and multivariate analysis. Results “Cases” were as, but not more, likely than “controls” to transmit. This was so whether transmission was measured in terms of the number of “cases” and smear-unmatched or -matched “controls” that had a secondary case, the number of secondary cases that they had or the number of new infections found in contacts of “cases” that died before treatment and their smear-matched “controls”. Conclusion In a low TB incidence/low HIV prevalence country, pulmonary TB patients that die a TB-related death before or in the initial phase of treatment and pulmonary TB patients that survive beyond the initial phase of treatment are equally likely to transmit.
Elements of Scientific Visualization in Basic Neuroscience Research

Abstract Scientific imaging systems have undergone a revolution over the last century since Wilhelm Röntgen's discovery of X rays in 1895. However, deciding which imaging system will do the job and assist in solving a scientific question—not just produce beautiful graphics with little practical use—can be difficult. This article serves as a minireview of methods and applications of imaging techniques for basic research. It identifies some of the popular types of imaging systems; describes briefly how they work; and illustrates their past, present, and potential future applications. It also attempts to identify inherent pitfalls associated with some of these systems. Finally, it demonstrates some of the specific applications of scientific imaging techniques in neuroscience research.
Somatic neurofibromatosis type 1 (NF1) inactivation characterizes NF1-associated pilocytic astrocytoma

Low-grade brain tumors (pilocytic astrocytomas) arising in the neurofibromatosis type 1 (NF1) inherited cancer predisposition syndrome are hypothesized to result from a combination of germline and acquired somatic NF1 tumor suppressor gene mutations. However, genetically engineered mice (GEM) in which mono-allelic germline Nf1 gene loss is coupled with bi-allelic somatic (glial progenitor cell) Nf1 gene inactivation develop brain tumors that do not fully recapitulate the neuropathological features of the human condition. These observations raise the intriguing possibility that, while loss of neurofibromin function is necessary for NF1-associated low-grade astrocytoma development, additional genetic changes may be required for full penetrance of the human brain tumor phenotype. To identify these potential cooperating genetic mutations, we performed whole-genome sequencing (WGS) analysis of three NF1-associated pilocytic astrocytoma (PA) tumors. We found that the mechanism of somatic NF1 loss was different in each tumor (frameshift mutation, loss of heterozygosity, and methylation). In addition, tumor purity analysis revealed that these tumors had a high proportion of stromal cells, such that only 50%–60% of cells in the tumor mass exhibited somatic NF1 loss. Importantly, we identified no additional recurrent pathogenic somatic mutations, supporting a model in which neuroglial progenitor cell NF1 loss is likely sufficient for PA formation in cooperation with a proper stromal environment.
An mRNA Stability Complex Functions with Poly(A)-Binding Protein To Stabilize mRNA In Vitro

ABSTRACT The stable globin mRNAs provide an ideal system for studying the mechanism governing mammalian mRNA turnover. α-Globin mRNA stability is dictated by sequences in the 3′ untranslated region (3′UTR) which form a specific ribonucleoprotein complex (α-complex) whose presence correlates with mRNA stability. One of the major protein components within this complex is a family of two polycytidylate-binding proteins, αCP1 and αCP2. Using an in vitro-transcribed and polyadenylated α-globin 3′UTR, we have devised an in vitro mRNA decay assay which reproduces the α-complex-dependent mRNA stability observed in cells. Incubation of the RNA with erythroleukemia K562 cytosolic extract results in deadenylation with distinct intermediates containing a periodicity of approximately 30 nucleotides, which is consistent with the binding of poly(A)-binding protein (PABP) monomers. Disruption of the α-complex by sequestration of αCP1 and αCP2 enhances deadenylation and decay of the mRNA, while reconstitution of the α-complex stabilizes the mRNA. Similarly, PABP is also essential for the stability of mRNA in vitro, since rapid deadenylation resulted upon its depletion. An RNA-dependent interaction between αCP1 and αCP2 with PABP suggests that the α-complex can directly interact with PABP. Therefore, the α-complex is an mRNA stability complex in vitro which could function at least in part by interacting with PABP.
A two layer disparity selective simple cell model

The responses of disparity selective complex cells in the mammalian visual system are often modeled by the disparity energy model. This model linearly combines inputs from binocular simple cell units, whose responses are computed by the combination of left and right eye inputs through linear binocular receptive fields, followed by half wave rectification and an expansive nonlinearity. While many complex cells have responses that can be modeled by the standard disparity energy model, there are many that cannot be. While the standard disparity energy model has been extended to account for some specific types of tuning (e.g. cells that are “monocularly responsive” in that they only respond to input from one eye, yet are disparity tuned indicating that they receive input from both eyes), actual neurons display a wider range of ocular dominance indices and disparity selectivities than can be fully accounted for by these models. Here, we describe a two layer simple cell model that can be used to construct complex cells that fully cover this range. The model combines the responses from a first layer of model monocular simple cells. By adjusting the weights from the monocular to a second binocular layer, the model can exhibit more diverse tuning properties than previously proposed models. We also show that these weights can be learned by sparse coding, and that if so, there is a strong relationship between distribution of tuning properties in the population and the input disparity statistics.
S18-1 Rapid evolutionary divergence of environment-dependent sexual traits in speciation: a paradox?

Expression of sexual displays is often closely linked to individual performance in a particular environment, i.e., male condition. Female preference for environment- and condition- dependent sexual displays in males evolves because of benefits of male condition to female fitness. Variation in these benefits can lead to divergence in female preferences that eventuate in speciation. To indicate condition reliably, sexual displays should have a significant environmental component in their development. Furthermore, mate preference favors a greater dependence on organismal functions in the development of ornaments (i.e., greater condition-dependence). Both environment- and condition-dependence might constrain evolutionary elaboration of the sexual trait as well as its effectiveness in achieving post-mating genetic isolation among divergent populations. Here we discuss an apparent paradox between the prevalent role of environment- and condition- dependent sexual displays in producing population divergence, and their expected slow rate of evolution.
Augmented Collaborative Spaces for Collective Sense Making: The Dicode Approach

Sense making is at the heart of cognitively complex and data intensive decision making processes. It is often conducted in collective spaces through exchange of ideas, discussions, analysing situations, and exploring alternatives. This position paper proposes a novel approach to facilitate collective sense making via a collaboration platform which (a) offers multiple views to collaboration (including forums, mind maps, and argumentation structure), and (b) provides intelligent support to understand sense making behaviour by employing user and community modelling techniques. The work is conducted in the framework of the EU funded Dicode project, developing intelligent services for data-intensive collaboration and decision making.
Moving Foreground Detection Based On Spatio-temporal Saliency

Detection of moving foreground in video is very important for many applications, such as visual surveillance, objectbased video coding, etc. When objects move with different speeds and under illumination changes, the robustness of moving object detection methods proposed so far is still not satisfactory. In this paper, we use the semantic information to adjust the pixel-wise learning rate adaptively for more robust detection performance, which are obtained by spatial saliency map based on Gaussian mixture model (GMM) in luma space and temporal saliency map obtained by background subtraction. In addition, we design a two-pass background estimation framework, in which the initial estimation is used for temporal saliency estimation, and the other is to detect foreground and update model parameters. The experimental results show that our method can achieve better moving object extraction performance than the existing background subtraction method based on GMM.
Robust and Real-time Rotation Estimation of Compound Omnidirectional Sensor

Camera ego-motion consists of translation and rotation, in which rotation can be described simply by distant features. We present a robust rotation estimation using distant features given by our compound omnidirectional sensor. Features are detected by a conventional feature detector, and then distant features are identified by checking the infinity on the omnidirectional image of the compound sensor. The rotation matrix is estimated between consecutive video frames using RANSAC with only distant features. Experiments with various environments show that our approach is robust and also gives reasonable accuracy in real-time.
Molecular Objects, Abstract Data Types, and Data Models: A Framework

Molecular objects occur frequently in CAD and engineering applications. At higher levels of abstraction they are treated as atomic unit,s of data; at lower levels they are defined in terms of a set of tuples possibly from different relations. System R’s complex objects are examples of molecular objects. In this paper, we present a framework for studying a generalized concept of molecular objects. We show that abstract data types unify this framework, which itself encompasses some recent data modeling contributions by researchers at IBM San Jose, Berkeley, Boeing, and Florida. A programming language/data structure paradigm is seen as a way of developing and testing the power of logical data models. A primary consequence of this paradigm is that future DBMSs must handle at least four distinct types of molecular objects: disjoint/non-disjoint and recursive/nonrecursive. No existing DBMS presently supports all these types.
Italian Society of Hematology practice guidelines for the management of iron overload in thalassemia major and related disorders

Three iron chelators are currently available for treatment of transfusion iron overload: deferoxamine, deferiprone, and deferasirox. This article reports the Italian Society of Hematology practice guidelines for the management of iron overload in thalassemia major and related disorders. New measures of iron accumulation in liver and heart (superconducting quantum inference device and magnetic resonance imaging), and oral iron chelators (deferiprone and deferasirox) are available for managing iron overload in thalassemia major. To assure appropriate use of these new health technologies, the Italian Society of Hematology appointed a panel of experts to produce clinical practice-guidelines for the management of iron overload in thalassemia major and related disorders. The analytical hierarchy process, a technique for multicriteria decision analysis, was applied to relevant key questions in order to identify the alternative strategies, generate explicit criteria for their evaluation, and check how well the alternatives fulfilled the criteria. The result of a comprehensive systematic review of articles released from 1990 to 2007 was used as a source of scientific evidence to compare the decisional options pairwise, and select the final recommendation. Every step in the model was developed from questionnaires and group discussion. The resulting recommendations advise about which examination to carry out in order to plan iron chelation therapy, when to start iron chelation, which iron chelator to choose in regularly transfused patients, how to monitor iron chelation therapy, and when and how to switch standard therapy.
Balancing Interests: Rethinking U.S. Selection of Skilled Immigrants

This study examines the selection of people admitted to the United States under the work-related categories of the U.S. immigration system. The contribution of both permanent and temporary economic-stream immigrants to the U.S. economy is first discussed. The authors outline the inadequacies of the present system in selecting the kind of foreign workers the country needs. Some alternative systems such as the points systems used by Canada and Australia are suggested as preferable to the current U.S. system; the details of a modified points system adapted to U.S. economic and labor-market realities are spelled out. The authors suggest that the proposed system will "help U.S. businesses to remain competitive in the global economy by facilitating access to the best foreign talent; (b) help U.S. workers by increasing opportunities for more and better jobs while protecting them from unfair competition; and (c) help immigrants to get a fair return on their investments in their own skills and expertise. " (EXCERPT)
Disease Modulation Leukocyte Galectin-1 Ligands and Immune Chimeric Molecule for Studying the Role of Development of a Nascent Galectin-1

Galectin-1 (Gal-1), a b -galactoside–binding lectin, plays a profound role in modulating adaptive immune responses by altering the phenotype and fate of T cells. Experimental data showing recombinant Gal-1 (rGal-1) efﬁcacy on T cell viability and cytokine production, nevertheless, is controversial due to the necessity of using stabilizing chemicals to help retain Gal-1 structure and function. To address this drawback, we developed a mouse Gal-1 human Ig chimera (Gal-1hFc) that did not need chemical stabilization for Gal-1 ligand recognition, apoptosis induction, and cytokine modulation in a variety of leukocyte models. At high concentrations, Gal-1hFc induced apoptosis in Gal-1 ligand + Th1 and Th17 cells, leukemic cells, and granulocytes from synovial ﬂuids of patients with rheumatoid arthritis. Importantly, at low, more physiologic concentrations, Gal-1hFc retained its homo-dimeric form without losing functionality. Not only did Gal-1hFc–binding trigger IL-10 and Th2 cytokine expression in activated T cells, but members of the CD28 family and several other immunomodulatory molecules were upregulated. In a mouse model of contact hypersensitivity, we found that a non-Fc receptor-binding isoform of Gal-1hFc, Gal-1hFc2, alleviated T cell-dependent inﬂammation by increasing IL-4 + , IL-10 + , TGF- b + , and CD25 high /FoxP3 + T cells, and by decreasing IFN- g + and IL-17 + T cells. Moreover, in human skin-resident T cell cultures, mutants containing substitutions in the AA-45 and/or AA-69 positions, validated the necessity of these residues for optimal functional activity. To examine Gal-1hFc effects in other effector leukocyte models, we found that granulocytes in inﬂamed joints of patients with rheumatoid arthritis (RA) were susceptible to Gal-1hFc–mediated cell death. In mice treatment with a non-Fc receptor-binding isoform of Gal-1hFc, Gal-1hFc2, suppressed hapten mediated contact hypersensitivity, by increasing IL-4 + , IL-10 + , TGF- b + , and CD25 high /FoxP3 + T cells and reducing IFN- g – and IL-17–producing T cells. Importantly, Gal-1hFc and Gal-1hFc2 elicited its T cell skewing, cell death, and cytokine modulation without the use of chemical stabilization approaches. These data support the use of Gal-1hFc and its mutants as new glycobiological tools for dissecting the roles of Gal-1 ligands on various immune processes.
Impact of Self-Administered Cocaine and Cocaine Cues on Extracellular Dopamine in Mesolimbic and Sensorimotor Striatum in Rhesus Monkeys

Studies were conducted to determine the impact of self-administered cocaine on extracellular striatal dopamine in four rhesus monkeys. The extent to which external cue conditioning contributed to the effects of cocaine and whether there is activation of striatal dopaminergic neurotransmission during drug-seeking behavior was also examined. Microdialysis measurements were made at 2 min intervals in sensorimotor (dorsolateral) and mesolimbic (central and ventromedial) striatum. A fixed-ratio schedule of reinforcement was used, with cocaine availability signaled by a visual cue. Studies examined the effects of cocaine or cocaine cues against a drug-free baseline. Large (fivefold to eightfold) increases in extracellular dopamine after a self-administered infusion of 0.5 mg/kg cocaine were quite rapid and matched the time course of reported subjective effects in human laboratory studies. To determine if conditioning to external cues contributed to the cocaine-induced increases, saline was substituted for cocaine in the infusion, leaving all other visual and auditory stimuli unchanged. No increase in extracellular dopamine in either sensorimotor or mesolimbic striatal subdivisions was observed. Extracellular dopamine during extended periods of drug-seeking behavior triggered by a visual cue was determined in both central and ventromedial striatum. This procedure also did not result in any measurable changes in extracellular dopamine. These studies demonstrate rapid and pronounced pharmacological actions of self-administered cocaine. No apparent conditioned component of those actions was associated with external environmental cues, suggesting that cues that trigger drug-seeking behavior in nonhuman primates do not cause conditioned increases in mesolimbic striatal dopamine.
Topological $K$-theory of equivariant singularity categories

We study the topological K-theory spectrum of the dg singularity category associated to a weighted projective complete intersection. We calculate the topological K-theory of the dg singularity category of a weighted projective hypersurface in terms of its Milnor fiber and monodromy operator, and, as an application, we obtain a lift of the Atiyah-Bott-Shapiro construction to the level of spectra.
A Sub-GHz Wireless Transmitter Utilizing a Multi-Class-Linearized PA and Time-Domain Wideband-Auto I/Q-LOFT Calibration for IEEE 802.11af WLAN

Broadband dynamic spectrum access in the sub-GHz band emerges as a potential solution for deploying low-cost range-enhanced wireless connectivity, suitable for under/less-developed countries. This paper describes a sub-GHz wireless transmitter (TX) with an integrated multi-class-linearized power amplifier (PA) compliant with the IEEE 802.11af wireless local-area network. It features a wideband in-phase/quadrature (I/Q) modulator exploiting two-stage 6-/14-path harmonic-rejection mixers plus G m- C low-pass filters to manage the spurs emission induced by hard-switched mixing. The entailed 8/16-phase local oscillator (LO) is generated by injection-locked phase correctors plus frequency dividers to relax the frequency and tuning range of the reference LO. The linearized PA features overdriven-class-A/B/C cells to balance the power efficiency and linearity; a dual-gate input pair to enlarge the linear gain range; and a wideband low-impedance ground at the second harmonic to suppress the harmonic distortion and ground bounces. The wideband I/Q imbalance and LO feedthrough are resolved by automatic digital calibration, which incorporates time-domain parameter estimation for better computational efficiency. Benchmarking with the recent art, this TX + PA solution fabricated in 65-nm CMOS exhibits higher system power efficiency (from 7.4% to 18.5%) and 1-dB compression point (from OP1 dB: + 12.5 to + 16.3 dBm). When delivering a 64-QAM orthogonal frequency division multiplexing signal at > + 10 dBm, the chip demonstrates sufficiently low noise floor ( -143 dBc/Hz), adjacent channel leakage ratio ( dB), and error vector magnitude fulfilling the specifications.
Assessing social security: Some useful results

This paper presents a dense summary of the most fundamental results on the issue of PAYG Social Security. They are presented in a simple and insightful analytical framework by working from the budget constraint of the household. The results presented in detail are a representation of the Aaron-Theorem, the equivalence of debt and Social Security, and a proof that under certain conditions the burden of Social Security on the current young and all future generations equals the benefit payments to the current old. Finally, I include uncertainty in the analysis and touch on the intergenerational risk-sharing implications of Social Security.
Pension Portability and Labor Mobility: Evidence from the Survey of Income and Program Participation

The evidence presented in this paper casts doubt on the proposition that pension backloading is responsible for the low job mobility rates observed for pension covered workers. It corroborates earlier findings by the authors, based on different data, that pension covered jobs offer higher levels of compensation than workers can obtain elsewhere, and it is this compensation premium, rather than non-portability, that accounts for lower turnover among pension covered workers. This evidence is further bolstered by the finding that defined contribution plans, which are not backloaded, and defined benefit plans, bear similar negative relations to mobility.
OPEC Behavior: A Test of Alternative Hypotheses

Since interpretations of past and future oil price patterns depends on the model chosen, the author tests and compares alternative theories of OPEC as a first step in validating the choice on any one model. The results show that among OPEC countries, the partial market-sharing cartel model is the only model not rejected by at least some of the 11 members and gives the best explanation of production. In comparison with 11 non-OPEC countries, the competitive model could not be rejected for 10 of the 11 non-OPEC producers. This raises the question of why, if OPEC is a cartel, Friedman's predictions have not come true, and introduces new questions for future research. 19 references, 3 tables.