Miracle-dz/UniFAR-FTUs huggingface dataset:
Rapid 3-D cone-beam reconstruction with the simultaneous algebraic reconstruction technique (SART) using 2-D texture mapping hardware

Algebraic reconstruction methods, such as the algebraic reconstruction technique (ART) and the related simultaneous ART (SART), reconstruct a two-dimensional (2-D) or three-dimensional (3-D) object from its X-ray projections. The algebraic methods have, in certain scenarios, many advantages over the more popular Filtered Backprojection approaches and have also recently been shown to perform well for 3-D cone-beam reconstruction. However, so far the slow speed of these iterative methods have prohibited their routine use in clinical applications. Here, the authors address this shortcoming and investigate the utility of widely available 2-D texture mapping graphics hardware for the purpose of accelerating the 3-D algebraic reconstruction. They find that this hardware allows 3-D cone-beam reconstructions to be obtained at almost interactive speeds, with speed-ups of over 50 with respect to implementations that only use general-purpose CPUs. However the authors also find that the reconstruction quality is rather sensitive to the resolution of the framebuffer, and to address this critical issue they propose a scheme that extends the precision of a given framebuffer by 4 bits, using the color channels. With this extension, a 12-bit framebuffer delivers useful reconstructions for 0.5% tissue contrast, while an 8-bit framebuffer requires 4%. Since graphics hardware generates an entire image for each volume projection, it is most appropriately used with an algebraic reconstruction method that performs volume correction at that granularity as well, such as SART or SIRT. The authors chose SART for its faster convergence properties.
Variability of Symbiodinium Communities in Waters, Sediments, and Corals of Thermally Distinct Reef Pools in American Samoa

Reef-building corals host assemblages of symbiotic algae (Symbiodinium spp.) whose diversity and abundance may fluctuate under different conditions, potentially facilitating acclimatization to environmental change. The composition of free-living Symbiodinium in reef waters and sediments may also be environmentally labile and may influence symbiotic assemblages by mediating supply and dispersal. The magnitude and spatial scales of environmental influence over Symbiodinium composition in different reef habitat compartments are, however, not well understood. We used pyrosequencing to compare Symbiodinium in sediments, water, and ten coral species between two backreef pools in American Samoa with contrasting thermal environments. We found distinct compartmental assemblages of clades A, C, D, F, and/or G Symbiodinium types, with strong differences between pools in water, sediments, and two coral species. In the pool with higher and more variable temperatures, abundance of various clade A and C types differed compared to the other pool, while abundance of D types was lower in sediments but higher in water and in Pavona venosa, revealing an altered habitat distribution and potential linkages among compartments. The lack of between-pool effects in other coral species was due to either low overall variability (in the case of Porites) or high within-pool variability. Symbiodinium communities in water and sediment also showed within-pool structure, indicating that environmental influences may operate over multiple, small spatial scales. This work suggests that Symbiodinium composition is highly labile in reef waters, sediments, and some corals, but the underlying drivers and functional consequences of this plasticity require further testing with high spatial resolution biological and environmental sampling.
Randomized Algorithms 2013 A Lecture 5 – Martingales , Closest Pairs , Hash Tables , Existential Proofs and Codes ∗

The question is whether these two requirements are equivalent and whether we can get the nice concentration for both of them. They are not equivalent as the following example shows. Consider a random walk on the integers with a reflecting wall at 0 where the first step chooses whether the walk is in the non negative or non positive integers. That is X0 = 0, the first step is random in {−1, 1} and all subsequent steps are random in {−1, 1} if Xi 6= 0 and reflect to the previous step if Xi = 0 (i.e. Xi+1 = Xi−1). Now the sequence is not a martingale according to (2), since given Xi, Xi−1 . X0, if Xi = 0 then we know that Xi+1 = Xi−1. But requirement (1) holds, since given Xi = 0 we have no idea whether we arrived from the positives or negatives. Under both definitions we have Azuma’s inequality: ∗These notes summarize the material covered in class, usually skipping proofs, details, examples and so forth, and possibly adding some remarks, or pointers. The exercises are for self-practice and need not be handed in. In the interest of brevity, most references and credits were omitted.
Passage Retrieval by Shrinkage of Language Models

Information retrieval is the process of searching for relevant documents that satisfy a user’s information need (usually in the form of queries). Some of its successful applications include library catalogue search, medical record retrieval, and Internet search engines (e.g., Google). As the exponential growth of web pages and online documents continues, there is an increasing need for retrieval systems that are capable of dealing with a large collection of documents and at the same time narrowing the scope of the search results (not only relevant documents but also relevant passages or even direct answers).
Interferon-alpha Induces High Expression of APOBEC3G and STAT-1 in Vitro and in Vivo

To investigate whether the JAK-STAT (Janus kinase-signal transducers and activators of transcription) pathway participates in the regulation of APOBEC3G (Apolipoprotein B mRNA-editing enzyme, catalytic polypeptide-like 3G) gene transcription and to study the molecular mechanisms of interferon resistance in patients with chronic hepatitis B (CHB), changes in APOBEC3G and STAT-1 expression levels in HepG2.2. 15 cells after treatment with various concentrations of IFN-α, were detected using real-time RT-PCR and Western-blot. In addition, the differences in STAT-1 and APOBEC3G expression in liver tissues were also observed in patients with different anti-viral responses to IFN-α. It is found that IFN-α suppressed HBV replication and expression markedly in HepG2.2. 15 cells, and simultaneously enhanced APOBEC3G expression in a dose- or time-dependent manner within a certain range. Moreover, a corresponding gradual increase in STAT-1 expression levels was also observed. The expression levels of STAT-1 and APOBEC3G in the liver of CHB patients with a complete response to IFN-α are significantly higher than that of the patients with non-response to IFN-α treatment. It is suggested that inducing intracellular APOBEC3G expression may be one of anti-HBV mechanisms of IFN-α, and IFN-α-induced APOBEC3G expression may be via the JAK-STAT signaling pathway. Moreover, interferon resistance may be related to the down-regulation of STAT-1 expression in the patients who had non-response to IFN-α treatment.
Discovering Piecewise Linear Models of Grid Workload

Despite extensive research focused on enabling QoS for grid users through economic and intelligent resource provisioning, no consensus has emerged on the most promising strategies. On top of intrinsically challenging problems, the complexity and size of data has so far drastically limited the number of comparative experiments. An alternative to experimenting on real, large, and complex data, is to look for well-founded and parsimonious representations. This study is based on exhaustive information about the gLite-monitored jobs from the EGEE grid, representative of a significant fraction of e-science computing activity in Europe. Our main contributions are twofold. First we found that workload models for this grid can consistently be discovered from the real data, and that limiting the range of models to piecewise linear time series models is sufficiently powerful. Second, we present a bootstrapping strategy for building more robust models from the limited samples at hand.
Improved Genetic Algorithm in SPICE OPUS for Model Parameter Extraction

SPICE is a widely used tool for simulation of analog circuits. Accurate models of devices are crucial for obtaining realistic results from the simulation. Although SPICE provides circuit designers with built-in models for most widely used devices many devices still must be modelled with subcircuit models in order to achieve sufficient accuracy. The hardest part of creating a SPICE model for a particular part is determining the parameter values of subcircuit elements. With analytical methods the problem quickly becomes impossible to manage. The only remaining alternative is optimisation. Use of SPICE OPUS optimisation capabilities for model parameter extraction is presented. Three commonly used optimisation methods are examined on examples and discussed in terms of their sensitivity to initial parameter values, speed and numeric stability.
Effects of atomicity and internal polarization on the electronic and optical properties of GaN/AlN quantum dots: Multimillion-atom coupled VFF MM-sp3 d5 s∗ tight-binding simulations

Single-particle electronic structure and optical transition rates between the HOMO and LUMO states of a self-organized wurtzite GaN/AlN single quantum dot grown along the [0001] axis are calculated within an atomistic 20-band sp3 d5 s* tight-binding framework. The GaN/AlN quantum dot used in this computational study is realistically-sized (containing ~9 million atoms) and of truncated pyramid shape having height and base length of 4.5 nm and 23 nm, respectively. These reduced-dimensionality III-N structures are subject to competing effects of size-quantization and long-range internal fields that originate from: a) fundamental crystal atomicity and the interface discontinuity between two dissimilar materials; b) atomistically strained active region; c) strain-induced piezoelectricity; and d) spontaneous polarization (pyroelectricity). The mechano-electrical internal fields in the structure have been modeled using a combination of an atomistic valence force-field molecular mechanics (VFF MM) approach and a three-dimensional Poisson solver, and have found to strongly modulate the intrinsic single-particle electronic and optical properties of the quantum dots. In particular, in contrast to the well-studied InN/GaN systems, the effects of piezoelectric and pyroelectric fields add up (peak pyroelectric potential being larger than the piezoelectric counterpart) and result in a large redshift in the electronic bandgap near the Brillouin zone center (known as quantum confined stark effect), pronounced non-degeneracy in the excited states, strongly suppressed optical transition (increased recombination time), and anisotropic emission spectra.
Towards lecture transcription in resource-scarce environments

We present progress towards automated Lecture Transcription (LT) in resource scarce environments. Our development has focused on the transcription of lectures in Afrikaans from two faculties at North-West University. A bootstrapping procedure is followed to filter and select well-aligned segments of speech. These segments are then used to train acoustic models. Initial work towards language modeling for LT in a resource-scarce environment is also presented; manual lecture transcriptions are combined with text mined from other sources such as study guides to train language models. Interpolation results indicate that study guides are a useful resource for language modeling, whereas general text (obtained from a publisher of Afrikaans books) is less useful in this context. Our findings are confirmed by the reduced word error rates (WERs) obtained from our off-line speech-recognition system for Lecture Transcription.
CARBOPLATIN DOSING FOR ADULT JAPANESE PATIENTS

ABSTRACT Carboplatin is a platinum-based anticancer drug that has been long used to treat many types of solid cancer. Because the clearance of carboplatin strongly correlates with the glomerular filtration rate (GFR), its dosage is calculated with the Calvert formula on the basis of the patient’s GFR to achieve the target area under the plasma drug concentration-time curve (AUC) for each patient. However, many lines of evidence from previous clinical studies should be interpreted with caution because different methods were used to estimate drug clearance and derive the dosage of carboplatin. There is a particularly high risk of carboplatin overdosing when the dosage is determined on the basis of standardized serum creatinine values. When deciding the dose of carboplatin for adult Japanese patients, preferred methods to assess renal function instead of directly measuring GFR include (1) 24-h urinary collection-based creatinine clearance adjusted by adding 0.2 mg/dl to the serum creatinine concentration measured by standardized methods, and (2) equation-based GFR (eGFR) with a back calculation to units of ml/min per subject. Given the limitations of serum creatinine-based GFR estimations, the GFR or creatinine clearance should be directly measured in each patient whenever possible. To ensure patient safety and facilitate a medical-team approach, the single most appropriate method available at each institute or medical team should be consistently used to calculate the dose of carboplatin with the Calvert formula.
Experimental treatment of stroke in spontaneously hypertensive rats by CD34+ and CD34- cord blood cells

Human umbilical cord blood as a source of stem cells has recently been reported in experimental treatment of cerebral disorders. However, little is known about the nature of cells and cellular mechanisms leading to neurofunctional improvement. Here we investigated the potential of separated CD34+ versus CD34- human umbilical cord blood cells (HUCBC) to promote functional recovery following stroke. The experiments were performed in spontaneously hypertensive (SH) rats, known for a risk profile comparable to stroke patients. After three weeks of behavioral training in the RotaRod and Beamwalk test arrays, stroke was induced by permanent middle cerebral artery occlusion (MCAO). For cell therapy, 1x106 cryopreserved cells were administered systemically between 8 and 10 hours after MCAO. The behavioral tests were performed together with a neurological severity score (mNSS) until day 29 to assess neurofunctional disabilities. Nearly complete functional remission was observed with both subpopulations CD34+ as well as CD34- cells. To localize cells histologically, they were labeled with a fluorescence dye (CFSE) before injection. Again, after administration of CD34+ as well as CD34- cells, CFSE labelled cells were found that accumulated in the border zone between the central necrosis of the ischemic lesion and functional brain tissue, thus indicating active attraction towards the lesion for both cell populations. Immunohistology with anti-CD68 and antibodies to human neuronal markers (NF-L, chromogranin) indicated an accumulation of human and rat monocytes in the border zone of the lesion while neuronal cells of human origin could not be detected in host brains.
Adverse Childhood Experiences and Adolescent Mental Disorders: Protective Mechanisms of Family Functioning, Social Capital, and Civic Engagement

This study aimed to investigate the protective effect of family functioning, social capital, and civic engagement on mental health in adolescents with adverse childhood experiences (ACEs). Parents of adolescents aged 12 to 17 years (N = 20,708) who participated in the 2015-2016 National Survey of Children’s Health were surveyed about their children’ ACEs (e.g., parental divorce, being a victim of violence, living with anyone who had substance abuse) and current mental health disorders, including depression, anxiety, and behavioral problems. Parents were further asked about their family functioning, perceived social capital, and adolescents’ civic engagement. Structural equation modeling was conducted to test the hypothesized pathways using Mplus 8.0. Based on parents’ report, about 55% of adolescents have experienced at least one kind of ACE. The final structural model proved an excellent fit to the data (CFI = 0.96, RMSEA = 0.009, WRMR = 1.12). A significantly positive relationship was found between adolescents’ ACEs and current mental disorders (β = 0.13, p < 0.05), and the effect was partially mediated by family functioning (β = 0.10, p < 0.001) and civic engagement (β = 0.01, p < 0.05), but not by social capital (β = 0.01, p = 0.12). Low household income (β = -0.24, p < 0.001) and low parent education (β = -0.05, p < 0.05) significantly increased adolescents’ likelihood of having ACEs. Early assessment and interventions for children with ACEs are necessary to prevent the development of mental disorders in adolescence, especially for minority adolescents and those of low socioeconomic status. Safe, nurturing, and supportive home and social environments can help mitigate the detrimental impact of childhood
Author's Personal Copy the Journal of Systems and Software Clpl: Providing Software Infrastructure for the Systematic and Effective Construction of Complex Collaborative Learning Systems Keywords: Software Architecture and Design Software Engineering Methods Software Reuse Component-based Software E

In most cases authors are permitted to post their version of the article (e.g. in Word or Tex form) to their personal website or institutional repository. Authors requiring further information regarding Elsevier's archiving and manuscript policies are encouraged to visit: a b s t r a c t Over the last decade, e-Learning and in particular Computer-Supported Collaborative Learning (CSCL) needs have been evolving accordingly with more and more demanding pedagogical and technological requirements. As a result, high customization and flexibility are a must in this context, meaning that col-laborative learning practices need to be continuously adapted, adjusted, and personalized to each specific target learning group. These very demanding needs of the CSCL domain represent a great challenge for the research community on software development to satisfy. This contribution presents and evaluates a previous research effort in the form of a generic software infrastructure called Collaborative Learning Purpose Library (CLPL) with the aim of meeting the current and demanding needs found in the CSCL domain. To this end, we experiment with the CLPL in order to offer an advanced reuse-based service-oriented software engineering methodology for developing CSCL applications in an effective and timely fashion. A validation process is provided by reporting on the use of the CLPL platform as the primary resource for the Master's thesis courses at the Open University of Catalonia when developing complex software applications in the CSCL domain. The ultimate aim of the whole research is to yield effective CSCL software systems capable of supporting and enhancing the current on-line collaborative learning practices.
The Path to Triacylglyceride Obesity in the sta6 Strain of Chlamydomonas reinhardtii

ABSTRACT When the sta6 (starch-null) strain of the green microalga Chlamydomonas reinhardtii is nitrogen starved in acetate and then “boosted” after 2 days with additional acetate, the cells become “obese” after 8 days, with triacylglyceride (TAG)-filled lipid bodies filling their cytoplasm and chloroplasts. To assess the transcriptional correlates of this response, the sta6 strain and the starch-forming cw15 strain were subjected to RNA-Seq analysis during the 2 days prior and 2 days after the boost, and the data were compared with published reports using other strains and growth conditions. During the 2 h after the boost, ∼425 genes are upregulated ≥2-fold and ∼875 genes are downregulated ≥2-fold in each strain. Expression of a small subset of “sensitive” genes, encoding enzymes involved in the glyoxylate and Calvin-Benson cycles, gluconeogenesis, and the pentose phosphate pathway, is responsive to culture conditions and genetic background as well as to boosting. Four genes—encoding a diacylglycerol acyltransferase (DGTT2), a glycerol-3-P dehydrogenase (GPD3), and two candidate lipases (Cre03.g155250 and Cre17.g735600)—are selectively upregulated in the sta6 strain. Although the bulk rate of acetate depletion from the medium is not boost enhanced, three candidate acetate permease-encoding genes in the GPR1/FUN34/YaaH superfamily are boost upregulated, and 13 of the “sensitive” genes are strongly responsive to the cell's acetate status. A cohort of 64 autophagy-related genes is downregulated by the boost. Our results indicate that the boost serves both to avert an autophagy program and to prolong the operation of key pathways that shuttle carbon from acetate into storage lipid, the combined outcome being enhanced TAG accumulation, notably in the sta6 strain.
An instruction timing model of CPU performance

A model of high-performance computers is derived from instruction timing formulas, with compensation for pipeline and cache memory effects. The model is used to predict the performance of the IBM 370/168 and the Amdahl 470 V/6 on specific programs,/and the results are verified by comparison with actual performance. Data collected about program behavior is combined with the performance analysis to highlight some of the problems with high-performance implementations of such architectures.
A Dynamic Approach to Information Quality in User-Generated Content

Information quality (IQ) plays a critical role in ecommerce consumers’ purchase decisions, and product-related user-generated content (PUGC) is an increasingly important source of information. Nevertheless, vendors currently do not take full advantage of PUGC since PUGC is mainly used for evaluation purposes. Integrating PUGC into earlier phases of the purchase-decision process might be promising. However, little is known about which dimensions of IQ consumers evaluate as being most important in different phases of the purchase process. To close this gap, we design a survey study that investigates the perceived relative importance of various IQ dimensions in each of three purchase phases (i.e., screening, filtering, and evaluation). Conceptually, we thus extend the concept of IQ to a dynamic approach. Practically, our findings can inform the design of ecommerce websites that integrate PUGC about how to best support the purchase-decision process with respect to dynamic IQ.
Sawtooth Software RESEARCH PAPER SERIES verview and Comparison of trategies for Choice-Based Conjoint Analysis

There are several different approaches to designing choice-based conjoint experiments and several kinds of effects one might want to model and quantify in such experiments. The approaches differ in terms of which effects they can capture and in how efficiently they do so. No single design approach is clearly superior in all circumstances. This paper describes different kinds of design formats (full profile, partial profile), and different methods for making designs (manual, computer optimization, computer randomization) for choice-based conjoint designs. Over and above the plain vanilla generic main effects most commonly modeled in conjoint analysis, there are several types of " special effects " that can be included in choice-based models. The various ways of constructing choice-based designs are compared in terms of their ability to capture these effects. Using simulations and artificial data sets we also assess the statistical efficiency of the various design methods.