Miracle-dz/UniFAR-FTUs huggingface dataset:
Four-Year Treatment Outcomes of Adult Patients Enrolled in Mozambique's Rapidly Expanding Antiretroviral Therapy Program

Background In Mozambique during 2004–2007 numbers of adult patients (≥15 years old) enrolled on antiretroviral therapy (ART) increased about 16-fold, from <5,000 to 79,500. All ART patients were eligible for co-trimoxazole. ART program outcomes, and determinants of outcomes, have not yet been reported. Methodology/Principal Findings In a retrospective cohort study, we investigated rates of mortality, attrition (death, loss to follow-up, or treatment cessation), immunologic treatment failure, and regimen-switch, as well as determinants of selected outcomes, among a nationally representative sample of 2,596 adults initiating ART during 2004–2007. At ART initiation, median age of patients was 34 and 62% were female. Malnutrition and advanced disease were common; 18% of patients weighed <45 kilograms, and 15% were WHO stage IV. Median baseline CD4+ T-cell count was 153/µL and was lower for males than females (139/µL vs. 159/µL, p<0.01). Stavudine, lamivudine, and nevirapine or efavirenz were prescribed to 88% of patients; only 31% were prescribed co-trimoxazole. Mortality and attrition rates were 3.4 deaths and 19.8 attritions per 100 patient-years overall, and 12.9 deaths and 57.2 attritions per 100 patient-years in the first 90 days. Predictors of attrition included male sex [adjusted hazard ratio (AHR) 1.5; 95% confidence interval (CI), 1.3–1.8], weight <45 kg (AHR 2.1; 95% CI, 1.6–2.9, reference group >60 kg), WHO stage IV (AHR 1.7; 95% CI, 1.3–2.4, reference group WHO stage I/II), lack of co-trimoxazole prescription (AHR 1.4; 95% CI, 1.0–1.8), and later calendar year of ART initiation (AHR 1.5; 95% CI, 1.2–1.8). Rates of immunologic treatment failure and regimen-switch were 14.0 and 0.6 events per 100-patient years, respectively. Conclusions ART initiation at earlier disease stages and scale-up of co-trimoxazole among ART patients could improve outcomes. Research to determine reasons for low regimen-switch rates and increasing rates of attrition during program expansion is needed.
Performance Evaluation Under Modeling Uncertainty: A Unified Approach Using Spherically Invariant Random Processes

In this dissertation, we considered the exceedingly general spherically invariant random process (SIRP) as a unifying framework for studying the wireless communication fading channels.In addition, we studied the important issue of modeling uncertainty, where only limited knowledge of the underlying fading channel statistics is known. The moment space methodology was proposed to characterize the uncertainty range of the system performance.Since performance evaluation for wireless communication systems frequently involve Monte Carlo simulation, we introduce the Super-Efficient Monte Carlo simulation methodology and the concept of Approximate Super-Efficiency (ASE) to improve the convergence rate of Monte Carlo simulation.While conventional Monte Carlo simulation yields the convergence rate $1/N$, our Super-Efficient Monte Carlo simulation has a superior convergence rate $1/N^2$ for integrands of the Super-Efficient type, and $1/N^{\alpha}$ for ASE algorithm, where $\alpha \in [1, 2]$. Finally, we studied the downlink throughput maximization problem in cellular networks.Inspired by the multi-armed bandit problem, we proposed several algorithms to solve the online throughput maximization problem, and provided convergence analysis.The proposed algorithms achieved up to 99\% of the performance upper bound within 1000 time steps.
Neural crest cell‐specific inactivation of Nipbl or Mau2 during mouse development results in a late onset of craniofacial defects

Nipbl (Scc2) and Mau2 (Scc4) encode evolutionary conserved proteins that play a vital role for loading the cohesin complex onto chromosomes, thereby ensuring accurate chromosome segregation during cell division. While mutations in human NIPBL are known to cause the developmental disorder Cornelia de Lange syndrome, the functions of Nipbl and Mau2 in mammalian development are poorly defined. Here we generated conditional alleles for both genes in mice and show that neural crest cell‐specific inactivation of Nipbl or Mau2 strongly affects craniofacial development. Surprisingly, the early phase of neural crest cell proliferation and migration is only moderately affected in these mutants. Moreover, we found that Mau2 single homozygous mutants exhibited a more severe craniofacial phenotype when compared to that of Nipbl;Mau2 double homozygous mutants. This raises the possibility that the Mau2/Nipbl protein interaction is not only required for cohesin loading, but may also be required to restrict the level of Nipbl involved in regulating gene expression. Together, the data suggest that proliferating neural crest cells tolerate a substantial reduction of cohesin loading proteins and we propose that the successive decrease of cohesin loading proteins in neural crest cells may alter developmental gene regulation in a highly dynamic manner. genesis 52:687–694, 2014. © 2014 Wiley Periodicals, Inc.
A national quitline service and its promotion in the mass media: modelling the health gain, health equity and cost–utility

Background Mass media campaigns and quitlines are both important distinct components of tobacco control programmes around the world. But when used as an integrated package, the effectiveness and cost-effectiveness are not well described. We therefore aimed to estimate the health gain, health equity impacts and cost–utility of the package of a national quitline service and its promotion in the mass media. Methods We adapted an established Markov and multistate life-table macro-simulation model. The population was all New Zealand adults in 2011. Effect sizes and intervention costs were based on past New Zealand quitline data. Health system costs were from a national data set linking individual health events to costs. Results The 1-year operation of the existing intervention package of mass media promotion and quitline service was found to be net cost saving to the health sector for all age groups, sexes and ethnic groups (saving $NZ84 million; 95%uncertainty interval 60–115 million in the base-case model). It also produced greater per capita health gains for Māori (indigenous) than non-Māori (2.2 vs 0.73 quality-adjusted life-years (QALYs) per 1000 population, respectively). The net cost saving of the intervention was maintained in all sensitivity and scenario analyses for example at a discount rate of 6% and when the intervention effect size was quartered (given the possibility of residual confounding in our estimates of smoking cessation). Running the intervention for 20 years would generate an estimated 54 000 QALYs and $NZ1.10 billion (US$0.74 billion) in cost savings. Conclusions The package of a quitline service and its promotion in the mass media appears to be an effective means to generate health gain, address health inequalities and save health system costs. Nevertheless, the role of this intervention needs to be compared with other tobacco control and health sector interventions, some of which may be even more cost saving.
Evaluation of mean residence time in subsurface waters using oxygen-18 fluctuations during drought conditions in the mid-Appalachians

Seasonal variations of the stable isotope, oxygen-18 (O), were used to estimate mean residence times of water in two Valley and Ridge Province watersheds in central Pennsylvania. Mean residence time was estimated by applying O input precipitation signatures to response function models that describe flow conditions in the subsurface system. Precipitation O is usually seasonally periodic; however, during this study period (3-98 to 6-99), unusual weather conditions and severe drought caused an abnormal seasonal signature in precipitation O. The atypical input precipitation amounts and O signatures required that adjustments be made using recharge factors and an extended past input function to represent the varying fraction of input water that contributed to turnover within the watershed during the study period. Oxygen18 variations were investigated in output waters from tension and zero-tension soil water lysimeters, shallow wells, and streamflow. Soil water O signatures were more responsive to precipitation O variations than streamflow O signatures. Theoretical models based on exponential piston-flow and dispersion flow processes fit data better than did other ground water age distribution models (i.e., pure piston flow or pure exponential models). Analysis suggested that during drought conditions, larger portions of older water dominated streamflow O composition, and that the current year’s precipitation O signature became more attenuated in the subsurface flow system. Mean residence times obtained for streamflow at each site were 9.5 and 4.8 months for a 14 and 100 ha watershed, respectively, and soil water mean residence time at 100 cm depth was on the order of a couple months; indicating a relatively rapid response of shallow ground water to precipitation.
A new definition of drowning: towards documentation and prevention of a global public health problem.

Drowning is a major global public health problem. Effective prevention of drowning requires programmes and policies that address known risk factors throughout the world. Surveillance, however, has been hampered by the lack of a uniform and internationally accepted definition that permits all relevant cases to be counted. To develop a new definition, an international consensus procedure was conducted. Experts in clinical medicine, injury epidemiology, prevention and rescue from all over the world participated in a series of "electronic" discussions and face-to-face workshops. The suitability of previous definitions and the major requirements of a new definition were intensely debated. The consensus was that the new definition should include both cases of fatal and nonfatal drowning. After considerable dialogue and debate, the following definition was adopted: "Drowning is the process of experiencing respiratory impairment from submersion/immersion in liquid. " Drowning outcomes should be classified as: death, morbidity, and no morbidity. There was also consensus that the terms wet, dry, active, passive, silent, and secondary drowning should no longer be used. Thus a simple, comprehensive, and internationally accepted definition of drowning has been developed. Its use should support future activities in drowning surveillance worldwide, and lead to more reliable and comprehensive epidemiological information on this global, and frequently preventable, public health problem.
Importance of Parenchymal: Stromal Cell Ratio for the Ex Vivo Reconstitution of Human Hematopoiesis

Many new developments in tissue engineering rely on the culture of primary tissues which is composed of parenchymal and mesenchymal (stromal) cell populations. Because stroma regulates parenchymal function, the parenchymal:stromal cell (P:S) ratio will likely influence culture behavior. To investigate parenchymal‐stromal cell interactions, the P:S ratio was systematically varied in a human bone marrow (BM) culture system, measuring the output of mature cells, immature progenitors (colony forming units‐granulocyte/macrophage [CFU‐GM]), and primitive stem cells (long‐term culture‐initiating cells [LTC‐IC]). When parenchymal CD34‐enriched cells were grown without stroma, cell and CFU‐GM output increased linearly as inoculum density was increased, resulting in constant cell and CFU‐GM expansion ratios. On irradiated preformed stroma (IPFS), culture output was significantly higher and less dependent on CD34‐enriched cell inoculum density, resulting in greater expansion ratios at lower inoculum densities. The number of IPFS cells required to support CD34‐enriched cells was independent of the CD34‐enriched cell number, suggesting that IPFS did not provide discrete niches, but instead acted through soluble signals. Experiments using conditioned medium (CM) from IPFS confirmed the presence of soluble signals, but CM did not completely substitute for direct contact between CD34‐enriched cells and IPFS. Because of known differences between IPFS and stroma growing within BM mononuclear cell (MNC) cultures, experiments were next performed using mixtures of CD34‐enriched and CD34‐depleted fractions of MNC. When inoculated with a fixed CD34+lin− cell number, culture output was optimal near the P:S ratio of the unmanipulated MNC sample and declined as CD34− cell number was increased or decreased. In cultures inoculated with a fixed total cell number, CFU‐GM output increased as CD34+lin− cell number was increased, whereas LTC‐IC output reached a plateau. These data suggest that a limited number of LTC‐IC supportive niches were present in MNC stroma, whereas IPFS lacks these niches and acts predominantly through a less potent soluble mechanism. These studies underscore the importance of parenchymal‐stromal cell interactions in the ex vivo reconstitution of tissue function and offer insight into the nature of these interactions in the human BM culture system.
Candidate Gene Analysis of Tooth Agenesis Identifies Novel Mutations in Six Genes and Suggests Significant Role for WNT and EDA Signaling and Allele Combinations

Failure to develop complete dentition, tooth agenesis, is a common developmental anomaly manifested most often as isolated but also as associated with many developmental syndromes. It typically affects third molars or one or few other permanent teeth but severe agenesis is also relatively prevalent. Here we report mutational analyses of seven candidate genes in a cohort of 127 probands with non-syndromic tooth agenesis. 82 lacked more than five permanent teeth excluding third molars, called as oligodontia. We identified 28 mutations, 17 of which were novel. Together with our previous reports, we have identified two mutations in MSX1, AXIN2 and EDARADD, five in PAX9, four in EDA and EDAR, and nine in WNT10A. They were observed in 58 probands (44%), with a mean number of missing teeth of 11.7 (range 4 to 34). Almost all of these probands had severe agenesis. Only few of the probands but several relatives with heterozygous genotypes of WNT10A or EDAR conformed to the common type of non-syndromic tooth agenesis, incisor-premolar hypodontia. Mutations in MSX1 and PAX9 affected predominantly posterior teeth, whereas both deciduous and permanent incisors were especially sensitive to mutations in EDA and EDAR. Many mutations in EDAR, EDARADD and WNT10A were present in several families. Biallelic or heterozygous genotypes of WNT10A were observed in 32 and hemizygous or heterozygous genotypes of EDA, EDAR or EDARADD in 22 probands. An EDARADD variant were in seven probands present together with variants in EDAR or WNT10A, suggesting combined phenotypic effects of alleles in distinct genes.
Design and Fabrication of a Magnetic Propulsion System for Self-Propelled Capsule Endoscope

This paper investigates design, modeling, simulation, and control issues related to self-propelled endoscopic capsule navigated inside the human body through external magnetic fields. A novel magnetic propulsion system is proposed and fabricated, which has great potential of being used in the field of noninvasive gastrointestinal endoscopy. Magnetic-analysis model is established and finite-element simulations as well as orthogonal design are performed for obtaining optimized mechanical and control parameters for generating appropriate external magnetic field. Simulated intestinal tract experiments are conducted, demonstrating controllable movement of the capsule under the developed magnetic propulsion system.
Shape statistics of Sloan Digital Sky Survey superclusters

We study the supercluster shape properties of the recently compiled Sloan Digital Sky Survey (SDSS) cluster catalogue using an approach based on differential geometry. We detect superclusters by applying the percolation algorithm to observed cluster populations, extended out to zmax≤ 0.23 in order to avoid selection biases. We utilize a set of shapefinders in order to study the morphological features of superclusters with ≥8 cluster members and find that filamentary morphology is the dominant supercluster shape feature, in agreement with previous studies.
Quantum Statistics: Is there an effective fermion repulsion or boson attraction?

Physicists often claim that there is an effective repulsion between fermions, implied by the Pauli principle, and a corresponding effective attraction between bosons. We examine the origins and validity of such exchange force ideas and the areas where they are highly misleading. We propose that explanations of quantum statistics should avoid the idea of an effective force completely, and replace it with more appropriate physical insights, some of which are suggested here.
Commitment to expression of the metalloendopeptidases, collagenase and stromelysin: relationship of inducing events to changes in cytoskeletal architecture

Agents that alter the morphology of rabbit synovial fibroblasts induce synthesis of the metalloendopeptidases, collagenase and stromelysin. We studied the relationship of cytoskeletal changes to the commitment to expression of these metalloendopeptidases. Cells treated with cytochalasin B (CB) or 12-O-tetradecanoylphorbol-13-acetate rounded, and only cells that had lost their stress fibers expressed collagenase and stromelysin, as determined by immunofluorescence. We concentrated on the effects of CB because of its rapid reversibility. When CB was added for 1-24 h, then removed, the cells respread within 30-60 min. The minimum period of CB treatment that committed cells to the subsequent synthesis of collagenase and stromelysin was 3 h. After initial treatment with 2 micrograms/ml CB for 3-24 h, or with various concentrations of CB (0-2 micrograms/ml) for 24 h, both enzyme activity and biosynthesis of the proenzymes showed a graded increase when measured at 24 h. Even after treatment with 2 micrograms/ml CB for only 3 h, greater than 85% of all cells were positive for both collagenase and stromelysin when cells were monitored by immunofluorescence. In contrast, when the dependence of collagenase and stromelysin expression on the inducing concentration of CB was examined, there was a dose- dependent increase in the number of cells positive for collagenase and stromelysin, as determined by immunofluorescence. Thus, at low concentrations of CB (less than 0.5 micrograms/ml), a heterogeneous population response was observed. These results suggest that the commitment of fibroblasts to induction of the metalloproteinases is a stochastic process in which a second signal that correlates with the disruption of the actin cytoskeleton may be rate-limiting for collagenase and stromelysin gene expression.
Salvage gamma knife radiosurgery in the management of dysembryoplastic neuroepithelial tumors: Long-term outcome in a single-institution case series

Background: Dysembryoplastic neuroepithelial tumors (DNT/DNET) are rare epileptogenic tumors. Microsurgery remains the best treatment option, although case reports exist on the use of gamma knife radiosurgery (GKRS) in selected cases. We investigated the long-term outcome of GKRS-treated DNTs at our institution in the context of current diagnostic and treatment options. Case Descriptions: We conducted a retrospective review of three consecutive adult patients (≥18 years) treated with salvage GKRS between 2002 and 2010 at Karolinska University Hospital, Stockholm, Sweden. The case series was supplemented by a review of current literature. A 20-year-old male underwent subtotal resection (STR) in 1997 and 2002 of DNT resulting in temporary control of intractable epilepsy despite antiepileptic drug treatment (AED). Long-term seizure control was obtained after GKRS of two separate residual DNT components along the surgical margin (2005 and 2010). A 27-year-old male undergoing gross total resection of the contrast-enhancing portion of a DNT (1999) resulted in temporary control of intractable epilepsy despite AEDs; lasting clinical control of seizures was achieved in 2002 after GKRS of a small, recurrent DNT component. A 28-year-old male underwent STR of DNT (1994 and 2004) resulting in temporary control of intractable epilepsy. Lasting seizure control was gained after GKRS of a residual tumor (2005). Conclusion: GKRS as performed in our series was effective in terms of tumor and seizure control. No adverse radiation effects were recorded. Prospective studies are warranted to establish the role of GKRS in the treatment of DNTs.
An interface for creating and manipulating curves using a high degree-of-freedom curve input device

Current interfaces for manipulating curves typically use a standard point cursor to indirectly adjust curve parameters. We present an interface for far more direct manipulation of curves using a specialized high degree-of-freedom curve input device, called ShapeTape. This device allows us to directly control the shape and position of a virtual curve widget. We describe the design and implementation of a variety of interaction techniques that use this curve widget to create and manipulate other virtual curves in 2D and 3D space. The input device is also used to sense a set of user gestures for invoking commands and tools. The result is an effective alternate user interface for curve manipulation that can be used in 2D and 3D graphics applications.
k-Means for Streaming and Distributed Big Sparse Data

We provide the first streaming algorithm for computing a provable approximation to the $k$-means of sparse Big data. Here, sparse Big Data is a set of $n$ vectors in $\mathbb{R}^d$, where each vector has $O(1)$ non-zeroes entries, and $d\geq n$. E.g., adjacency matrix of a graph, web-links, social network, document-terms, or image-features matrices. Our streaming algorithm stores at most $\log n\cdot k^{O(1)}$ input points in memory. If the stream is distributed among $M$ machines, the running time reduces by a factor of $M$, while communicating a total of $M\cdot k^{O(1)}$ (sparse) input points between the machines. % Our main technical result is a deterministic algorithm for computing a sparse $(k,\epsilon)$-coreset, which is a weighted subset of $k^{O(1)}$ input points that approximates the sum of squared distances from the $n$ input points to every $k$ centers, up to $(1\pm\epsilon)$ factor, for any given constant $\epsilon>0$. This is the first such coreset of size independent of both $d$ and $n$. Existing algorithms use coresets of size at least polynomial in $d$, or project the input points on a subspace which diminishes their sparsity, thus require memory and communication $\Omega(d)=\Omega(n)$ even for $k=2$. Experimental results real public datasets shows that our algorithm boost the performance of such given heuristics even in the off-line setting. Open code is provided for reproducibility.
Linear buckling analysis of welded girder webs with variable thickness

Steel girder web panels have been subjected in recent decades, to a number of experimental and numerical studies but the mechanisms that regulate the behaviour of the panels composed by two subpanels with different thickness were not deeply studied. Furthermore specific design rules regarding the estimation of the buckling coefficient for panels with variable thickness are not included in the codes even if this is a common situation particularly for steel bridge girders with beams having significant height. In this framework,this work aims to investigate buckling behaviour of steel beams with webs composed of panels with different thicknesses subjected to both in-plane axial compression and bending moment and gives some simplified equations for the estimation of the buckling coefficient.