Miracle-dz/UniFAR-FTUs huggingface dataset:
Bayesian modeling for large spatial datasets

We focus upon flexible Bayesian hierarchical models for scientific data available at geo‐coded locations. Investigators are increasingly turning to spatial process models to analyze such datasets. These models are customarily estimated using Markov Chain Monte Carlo (MCMC) methods, which have become especially popular for spatial modeling, given their flexibility and power to fit models that would be infeasible otherwise. However, estimating Bayesian spatial process models is undermined by prohibitive computational expenses associated with parameter estimation. Classes of low‐rank spatial process models are increasingly being deployed to resolve this problem by projecting spatial effects to a lower‐dimensional subspace. We discuss how a low‐rank process called the ‘predictive process’ seamlessly enters the hierarchical modeling framework and helps us accrue substantial computational benefits. WIREs Comp Stat 2012, 4:59–66. doi: 10.1002/wics.187
Room layout estimation from rapid omnidirectional exploration

A new generation of practical, low-cost indoor robots is now using wide-angle cameras to aid navigation, but usually this is limited to position estimation via sparse feature-based SLAM. Such robots usually have little global sense of the dimensions, demarcation or identities of the rooms they are in, information which would be very useful to enable behaviour with much more high level intelligence. In this paper we show that we can augment an omni-directional SLAM pipeline with straightforward dense stereo estimation and simple and robust room model fitting to obtain rapid and reliable estimation of the global shape of typical rooms from short robot motions. We have tested our method extensively in real homes, offices and on synthetic data. We also give examples of how our method can extend to making composite maps of larger rooms, and detecting room transitions.
High linearity voltage-controlled oscillator

A linearization technique for CMOS voltage-controlled oscillators (VCOs) is presented. The linearity of the oscillator is improved by applying a feedback loop using a switched-capacitor network as a frequency-to-voltage converter (FVC). The technique is verified by circuit-level simulation using parameters of a 0.35-µm CMOS technology. After the linearization, the linearity error of VCO can be improved to less than 0.015% for a dynamic range of 60 dB.
Qualitative Simulation as a Temporally-extended Constraint Satisfaction Problem

Traditionally, constraint satisfaction problems (CSPs) are characterized using a finite set of constraints expressed within a common, shared constraint language. When reasoning across time, however, it is possible to express both temporal and state-based constraints represented within multiple constraint languages. Qualitative simulation provides an instance of this class of CSP in which, traditionally, all solutions to the CSP are computed. In this paper, we formally describe this class of temporally-extended CSPs and situate qualitative simulation within this description. This is followed by a description of the DecSIM algorithm which is used to incrementally generate all possible solutions to a temporally-extended CSP. DecSIM combines problem decomposition, a tree-clustering algorithm and ideas similar to directed arc--consistency to exploit structure and causality within a qualitative model resulting in an exponential speed-up in simulation time when compared to existing techniques.
Reconfigurable LUT: Boon or Bane for Secure Applications

Modern FPGAs offer various new features for enhanced reconfigurability and better performance. One of such feature is a dynamically Reconfigurable LUT (RLUT) whose content can be updated internally, even during run-time. There are many scenarios like pattern matching where this feature has been shown to enhance performance of the system. In this paper, we study RLUT in the context of secure applications. Next, we design several case-studies to apply this feature on security critical scenarios. These case-studies vary from destructive scenarios like stealthy hardware Trojans to constructive scenarios like implementation of secret ciphers with custom Sboxes and masking countermeasure.
Fast On-Line Speech/Voiceband - Data Discrimination for Statistical Multiplexing of Data with Telephone Conversations

This paper concerns the design of a speech/data discriminator with the speed and accuracy required for statistical multiplexing of speech and high-speed baseband data on a single telephone line. The structure proposed for the discriminator combines the information from two parallel processes. The first process, even though slow, accurately recognizes the speech/data nature of the signal. This nature is determined by statistical pattern classification applied to simple zero-crossing-type parameters extracted from the signal filtered in a PCM representation. The second process has temporal accuracy in detecting transition events, from speech to data and vice versa. This detection is provided by special parameters which supply tentative transition markers. This paper applies these processes to the case of 9600 bit/s modems and describes a complete discrimination algorithm which is fit for microprocessor technology. The simulation results provided indicate a very low error rate and demonstrate that transitions are detected exactly or within one or two sampling intervals.
Sexual and marital trajectories and HIV infection among ever-married women in rural Malawi

Objective: To explore how sexual and marital trajectories are associated with HIV infection among ever-married women in rural Malawi. Methods: Retrospective survey data and HIV biomarker data for 926 ever-married women interviewed in the Malawi Diffusion and Ideational Change Project were used. The associations between HIV infection and four key life course transitions considered individually (age at sexual debut, premarital sexual activity, entry into marriage and marital disruption by divorce or death) were examined. These transitions were then sequenced to construct trajectories that represent the variety of patterns in the data. The association between different trajectories and HIV prevalence was examined, controlling for potentially confounding factors such as age and region. Results: Although each life course transition taken in isolation may be associated with HIV infection, their combined effect appeared to be conditional on the sequence in which they occurred. Although early sexual debut, not marrying one’s first sexual partner and having a disrupted marriage each increased the likelihood of HIV infection, their risk was not additive. Women who both delayed sexual debut and did not marry their first partner are, once married, more likely to experience marital disruption and to be HIV-positive. Women who marry their first partner but who have sex at a young age, however, are also at considerable risk. Conclusions: These findings identify the potential of a life course perspective for understanding why some women become infected with HIV and others do not, as well as the differentials in HIV prevalence that originate from the sequence of sexual and marital transitions in one’s life. The analysis suggests, however, the need for further data collection to permit a better examination of the mechanisms that account for variations in life course trajectories and thus in lifetime probabilities of HIV infection.
Increased plasma levels of interleukin-6 in sepsis.

Interleukin-6 (IL-6) is likely to be an important mediator of the inflammatory response. We measured levels of this cytokine in plasma samples from 37 patients with sepsis or septic shock obtained at the time of admission to the intensive care unit and related these levels to hemodynamic and biochemical parameters as well as to clinical outcome. In 32 of the 37 patients, increased levels of IL-6 were found, occasionally up to 7,500 times the normal level. The highest IL-6 levels were encountered in patients who suffered from septic shock (P value of the difference between patients with and without shock less than .0001). In addition, IL-6 significantly correlated with plasma lactate (P less than .0001), heart rate (P = .05) and, inversely, with mean arterial pressure (P = .01) and platelet counts (P = .0002). Significant correlations of IL-6 with the anaphylatoxins C3a (P = .0001) and C4a (P = .0002) and with the main inhibitor of the classical pathway of complement, C1-inhibitor (inverse correlation, P = .05), were also observed. IL-6 on admission appeared to be of prognostic significance: levels were higher in septic patients who subsequently died than in those who survived (P = .0003), in particular when only patients with septic shock were considered (P less than .0001). All nine septic patients with levels of less than 40 U/mL on admission survived, whereas 89% of the nine patients with levels exceeding 7,500 U/mL died. These data provide evidence for a role of IL-6 in the pathophysiology of septic shock. Further studies are needed to reveal whether IL-6 in sepsis is directly involved in mediating lethal complications or whether it is to be considered as an "alarm hormone" that reflects endothelial cell injury probably mediated by the anaphylatoxines.
The culture of the industry and the culture of research

Culture is increasingly cited as being in need of change if the UK construction industry is to improve its efficiency and productivity. The paper argues that the concept of culture is amenable to radically different treatments and that the research community must recognize the consequences of this choice if it is to make a useful contribution to bringing about the desired change. The dominant research paradigm in construction management is examined and compared to an alternative approach. The consequences attendant upon the choice between these two are explored with reference to four phenomena: a study of quality in the construction industry, Japanese innovation in management, Deming's concept of total quality management and the situation of the site engineer. It is concluded that the dominant rationalist paradigm tacitly endorses existing attitudes and that if researchers are to have a role in changing the culture of the industry, then the culture of research must change also.
Ultrasound based evaluation of hepatic steatosis and fibrosis in hepatitis C non-responders.

OBJECTIVE To determine the accuracy of ultrasound in the diagnosis and grading of steatosis and fibrosis in Hepatitis C (HCV) patients not responding to ribavarin-interferon therapy. STUDY DESIGN A cross-sectional, analytical study. PLACE AND DURATION OF STUDY Radiology Department, Civil Hospital, Karachi, from March 2008 to August 2010. METHODOLOGY Patients with positive HCV RNA despite 24 weeks ribavarin-interferon therapy (non-responders) were subjected to ultrasound and biopsy prior to institution of pegylated interferon therapy for detection and grading of steatosis and fibrosis. Using histopathology as the gold standard, sensitivity, specificity, negative and positive predictive values for ultrasound were determined. RESULTS The sensitivity of ultrasound for hepatic steatosis was 90.9% for no steatosis (NS), 100% for moderate and gross steatosis and 84.4% for mild steatosis with 100% specificity. The sensitivity for fibrosis was 25% for no fibrosis, 100% for mild fibrosis, 89.74% for moderate fibrosis and 100% for gross fibrosis. The overall accuracy for detection of steatosis was 95.39% and that for fibrosis was 98.02%. Hepatic vein showed increased dampening of flow with advancing grades of steatosis and fibrosis. CONCLUSION Ultrasound has a high accuracy in the diagnosis and grading of steatosis and fibrosis in HCV nonresponders. Mild fibrosis may confound the diagnosis of mild steatosis.
Enhancement of photophysical properties and deterministic transfer of quantum emitters in hexagonal boron nitride

Color centers in solid state crystals have become a frequently used system for single photon generation, advancing the development of integrated photonic devices for quantum optics and quantum communication applications. In particular, defects hosted by two-dimensional (2D) hexagonal boron nitride (hBN) are a promising candidate for next-generation single photon sources, due to its chemical and thermal robustness and high brightness at room temperature. The 2D crystal lattice of hBN allows for a high extraction efficiency and easy integration into photonic circuits. Here we develop plasma etching techniques with subsequent high temperature annealing to reliably create defects. We show how different fabrication parameters influence the defect formation probability and the emitter brightness. A full optical characterization reveals improved quality of the created quantum emitters, represented by a narrow spectrum, short excited state lifetime, high purity and photostability over long periods. We utilize a wet chemically-assisted transfer process to reliably transfer the single photon sources onto arbitrary substrates, demonstrating the feasibility for the integration into scalable photonic quantum information processing networks.
Some determinants of clinical evaluations of different psychiatrists.

The use of the interview as a diagnostic technique continues in spite of the many questions raised about its reliability and validity. There is a subjective feeling of comfort and security to be had from seeing and talking with a person which persists even when the information gained, translated, and sorted into ratings, predictions, and the like, fails to correlate with other variables (Kelly and Fiske, 3 1951). Those who feel that the interview has little value state that in an unstructured situation there is too great a danger that the interviewer will be biased by his own needs and attitudes. Robinson and Cohen 5 (1954) found reliable differences in the case reports of interns in clinical psychology which were related to the personality characteristics of the interns, and somewhat similar results were reported by Raines and Rohrer 4 (1955) in a study of psychiatrists’ ratings of Naval
Curvature-based transfer functions for direct volume rendering: methods and applications

Direct volume rendering of scalar fields uses a transfer function to map locally measured data properties to opacities and colors. The domain of the transfer function is typically the one-dimensional space of scalar data values. This paper advances the use of curvature information in multi-dimensional transfer functions, with a methodology for computing high-quality curvature measurements. The proposed methodology combines an implicit formulation of curvature with convolution-based reconstruction of the field. We give concrete guidelines for implementing the methodology, and illustrate the importance of choosing accurate filters for computing derivatives with convolution. Curvature-based transfer functions are shown to extend the expressivity and utility of volume rendering through contributions in three different application areas: nonphotorealistic volume rendering, surface smoothing via anisotropic diffusion, and visualization of isosurface uncertainty.
Mechanochemically Metamorphosed Composites of Homogeneous Nanoscale Silicon and Silicate Oxides with Lithium and Metal Compounds

An active anode material for Li-ion batteries was synthesized using a simple mechanochemical process to minimize the large change in Si volume observed during charge-discharge operation and to compensate for the associated irreversible loss of Li or irreversible capacity loss, which are obstacles to achieve high-performance electrochemical properties during charge-discharge. The composite was mechanochemically milled with Si, lithium oxide, and copper oxide as raw materials; the composite contains Si nanoparticles, amorphous silicon monoxide, and Si-Li or Si-Cu alloy compounds, and it exhibits improved electrochemical properties. In particular, this composite achieved a better capacity retention, higher coulombic efficiency (over 100%), and longer cycling performance than Si alone, indicating considerable optimization of the electrical and ionic conductivity in the composite. The developed method allowed for control of the Li content to compensate for the lack of Li ions in the composite, and the cycling performance was optimized using the Cu alloy, oxide, and Li compounds within the composite.
Interstitial Voids and Resultant Density of Liquid Water: A First-Principles Molecular Dynamics Study

Many anomalous properties of water can be explained on the basis of the coexistence of more than one density states: high-density water (HDW) and low-density water (LDW). We investigated these two phases of water molecules through first-principles molecular dynamics simulations using density functional theory (DFT) in conjunction with various van der Waals-corrected exchange and correlation functionals. Different density regions were found to exist due to the difference in short-range and long-range forces present in DFT potentials. These density regions were identified and analyzed on the basis of the distribution of molecules and voids present. We defined a local structure index to distinguish and find the probability of occurrence of these different states. HDW and LDW arise due to the presence of “interstitial water” molecules in between the first and second coordination shells. The population of interstitial water molecules is found to affect the overall dynamics of the system as they change the hydrogen bond pattern.
Identification of an essential gene responsible for d‐Asp incorporation in the Lactococcus lactis peptidoglycan crossbridge

Bacteria such as Lactococcus lactis have d‐aspartate (d‐Asp) or its amidated derivative d‐asparagine (d‐Asn), in their peptidoglycan (PG) interpeptide crossbridge. We performed a subtractive genome analysis to identify L. lactis gene yxbA, orthologues of which being present only in bacteria containing d‐amino acids in their PG crossbridge, but absent from those that instead insert l‐amino acids or glycine. Inactivation of yxbA required a complementing Streptococcus pneumoniae murMN genes, which express enzymes that incorporate l‐Ser‐l‐Ala or l‐Ala‐l‐Ala in the PG crossbridge. Our results show that (i) yxbA encodes d‐Asp ligase responsible for incorporation of d‐Asp in the PG crossbridge, and we therefore renamed it as aslA, (ii) it is an essential gene, which makes its product a potential target for specific antimicrobials, (iii) the absence of d‐Asp may be complemented by l‐Ser‐l‐Ala or l‐Ala‐l‐Ala in the L. lactis PG, indicating that the PG synthesis machinery is not selective for the side‐chain residues, and (iv) lactococcal strains having l‐amino acids in their PG crossbridge display defects in cell wall integrity, but are able to efficiently anchor cell wall proteins, indicating relative flexibility of lactococcal transpeptidation reactions with respect to changes in PG side‐chain composition.
Nivolumab as Programmed Death-1 (PD-1) Inhibitor for Targeted Immunotherapy in Tumor

Targeted immunotherapy has become the most promising approach for tumor patients. Programmed death-1 (PD-1), an inhibitory receptor expressed on activated T cells, can reverse immune suppression and release T cell activation. Nivolumab, a fully human immunoglobulin G4 PD-1 immune checkpoint inhibitor antibody, blocks PD-1 and promotes antitumor immunity, and it is effective for treating non-small-cell lung cancer (NSCLC), melanoma, renal cell carcinoma (RCC) and other cancers. The present review summarizes the efficacy and current status of clinical trials of nivolumab and that enabled nivolumab to be investigated in patients.
Insulin-like growth factor I receptor signaling in transformation by src oncogenes

R- cells, a line of mouse embryo fibroblasts with a targeted disruption of the insulin-like growth factor I (IGF-I) receptor genes, are refractory to transformation by several viral and cellular oncogenes. Using colony formation in soft agar as a measure of full transformation, we report here that R- cells can be transformed by v-src, although they still cannot be transformed by the activated c-src527 (mutation at tyrosine 527 to phenylalanine), which readily transforms mouse embryo cells with a wild-type number of IGF-I receptors (W cells). Although v-src is a more potent inducer of tyrosine phosphorylation than c-src527, the extent of phosphorylation of either insulin receptor substrate 1 or Shc, two of the major substrates of the IGF-I receptor, does not seem sufficiently different to explain the qualitative difference in soft agar growth. v-src, however, is considerably more efficient than c-src527 in its ability to tyrosyl phosphorylate, in R- cells, the focal adhesion kinase, Stat1, and p130cas. These results indicate that v-src, but not c-src527, can bypass the requirement for a functional IGF-I receptor in the full transformation of mouse embryo fibroblasts and suggest that qualitative and quantitative differences between the two oncogenes can be used to identify some of the signals relevant to the mechanism(s) of transformation.
Controlling bloating using depth constraint crossover

We develop a simple modification of crossover called depth constraint crossover to control bloating. As the name suggests, depth constraint crossover adds a depth constraint on the selection of crossover point. This method is motivated by the analysis of removal bias bloating theory. In this paper, we quantitatively define removal bias as the depth difference between swapped subtrees in crossover. Experiments show that the removal bias defined can be widely observed in GP problems and it is strongly correlated to the growth of population size. We find that by limiting the maximum depth difference between subtrees swapped in crossover with depth constraint crossover, it is possible to greatly reduce the removal bias and hence effectively control bloating. To analyze the efficiency of depth constraint crossover, we compare the technique with koza-style depth limiting method on four different problem domains. Experiment results show that the new technique are very effective in controlling bloating while still maintaining fitness.
Histidines 578 and 587 in the S5-S6Linker of the Human Ether-a-gogo Related Gene-1K+ Channels Confer Sensitivity to Reactive Oxygen Species*

The K+ channels encoded by the human Ether-a-gogo Related Gene-1 (hERG1) are crucially involved in controlling heart and brain excitability and are selectively influenced by reactive oxygen species (ROS). To localize the molecular regions involved in ROS-induced modulation of hERG1, segmental exchanges between the ROS-sensitive hERG1 and the ROS-insensitive bovine ether-a-gogo gene (bEAG) K+ channels were generated, and the sensitivity of these chimeric channels to ROS was studied with the two-microelectrode voltage-clamp technique upon their expression in Xenopus oocytes. Substitution of the S5-S6 linker of hERG1 with the corresponding bEAG region removed channel sensitivity to ROS, whereas the reverse chimeric exchange introduced ROS sensitivity into bEAG. Mutation of each of the two hERG1 histidines at positions 578 and 587 within the S5-S6 linker generated K+ channels insensitive to modulation by ROS. In addition, the two iron chelators desferrioxamine (1 mm) and o-phenanthroline (0.2 mm) significantly inhibited hERG1 outward K+ currents and prevented hERG1 inhibition induced by the ROS-scavenging enzyme catalase (1000 units/ml). Finally, the hERG1-inhibitory effect exerted by the iron chelators was prevented by the hERG1 H578D/H587Y double mutation. Collectively, the results obtained suggest that histidines at positions 578 and 587 in the S5-S6 linker region of hERG1 K+channels are crucial players in ROS-induced modulation of hERG1 K+ channels.