Miracle-dz/UniFAR-FTUs huggingface dataset:
Parallelizing the XSTAR Photoionization Code

We describe two means by which XSTAR, a code which computes physical conditions and emission spectra of photoionized gases, has been parallelized. The first is pvm_xstar, a wrapper which can be used in place of the serial xstar2xspec script to foster concurrent execution of the XSTAR command line application on independent sets of parameters. The second is PModel, a plugin for the Interactive Spectral Interpretation System (ISIS) which allows arbitrary components of a broad range of astrophysical models to be distributed across processors during fitting and confidence limits calculations, by scientists with little training in parallel programming. Plugging the XSTAR family of analytic models into PModel enables multiple ionization states (e.g., of a complex absorber/emitter) to be computed simultaneously, alleviating the often prohibitive expense of the traditional serial approach. Initial performance results indicate that these methods substantially enlarge the problem space to which XSTAR may be applied within practical timeframes.
Fault Tolerant Control for Polynomial Linear Parameter Varying (LPV) Systems applied to the stabilization of a riderless bicycle

This paper presents the results of a Fault Tolerant Control based on observers for polynomial LPV systems. The main contribution lies in observers, controller, Fault Diagnosis and Isolation unit and Fault Tolerant Control (FTC) design procedure, based on the solution of Parameterized Linear Matrix Inequalities (PLMI) with application to a riderless bicycle dynamics. Further, unlike previous works, this approach takes for its design only the measured outputs provided by the in-built bicycle prototype sensors, eliminating the necessity of additional computations for the control law. The previous fact is viewed as an additional contribution in this development.
A Cross-Layer Vertical Handover Decision Model for Heterogeneous Wireless Networks

Vertical handover in heterogeneous wireless networks is a strategic decision due to its profound impact on mobile applications and their performance. Primarily it's an issue of network availability and secondarily it is a question of choosing best available service. This paper presents a Cross-layer Vertical Handover (CVH) decision model that maintains the pre-decision load of vertical handover processing on two layers i.e. application layer and a thin shim layer between the network and data link layer. A matchmaker service help in handover decision on the basis of best match of application demands with available connectivity options. The results show low-latency, highly consistent vertical handovers during mobility and improved performance of applications with respect to throughput and reliability.
What kinds of things cause children’s reading difficulties?

The first part of this paper explains the distinction between proximal and distal causes of developmental disorders of cognition, with special reference to developmental disorders of reading. A number of different proximal causes of developmental disorders of reading have been identified. These correspond to a number of different patterns of developmental reading impairments – a number of “types of developmental dyslexia”, if you like – which are described in the second part of the paper. These patterns are interpreted in relation to a specific information-processing model of the cognitive system for reading. How each pattern is diagnosed, and how each might be treated, is discussed.
Hierarchical Compression of Tetrahedral Meshes Through Clustering and Vector Quantization

To visualize the unstructured volumetric and surface data Delaunay triangulation is utilised which results in the formation of tetrahedral meshes. These generated tetrahedral meshes possessing Delaunay topology, facilitates the progressive transmission design and coding. Two or three levels of detail of the same data can be acquired by implementation of hierarchical decimation over these meshes. These data sets are then sent to Encoder for compression. A new scheme for geometry data compression has been devised in this paper. Compression algorithm is composed of three stages. Initially centroids and the frequencies are determined by clustering. Then error vectors are generated by deducting vertex location from centroids. To exploit the statistical dependency of these error vectors vector quantization is employed over them in the third and final stage. The compression scheme, progressive transmission and quality of meshes are scalable.
Smaller Cigarette Pack as a Commitment to Smoke Less? Insights from Behavioral Economics

Cigarettes are commonly sold in packs of 20 units and therefore little is known about the potential impact of pack size on consumption. Using insights from behavioral economics, we suggest that cigarette packs smaller than the standard size may help some smokers cut back and/or quit, consistent with their long-term goals. Results from an online hypothetical purchase experiment conducted in a sample of US smokers reveal that over a third of smokers are willing to pay a price premium to purchase in smaller quantities. Further, a desire to quit smoking and high self-control is associated with preference for a smaller pack. While we provide some preliminary evidence that smaller packs may be beneficial to certain types of smokers, further research should be conducted to assess whether the smaller pack size should be considered in the arsenal of tobacco control policies to help current smokers quit (JEL: I18; I12; D12)
First principles study of phosphorus and boron substitutional defects in Si-XII

We present a first principles study of boron and phosphorus substitutional defects in Si-XII. Recent results from nanoindentation experiments reveal that the Si-XII phase is semiconducting and has the interesting property that it can be doped n- and p-type at room temperature without an annealing step. Using the hybrid functional of Heyd, Scuseria and Ernzerhof (HSE), we examine the formation energies of the B and P defects at the two distinct atomic sites in Si-XII to find on which site the substitutional defects are more easily accommodated. We also estimate the thermodynamic transition levels of each defect in its relevant charge states. The hybrid calculations also give an independent prediction that Si-XII is semiconducting, in agreement with recent experimental data.
Detection of human papillomavirus in cervical lymph nodes: a highly effective strategy for localizing site of tumor origin.

PURPOSE Patients with head and neck squamous cell carcinoma (HNSCC) often come to clinical attention with a neck mass due to metastatic spread to lymph nodes. Treatment is dictated by the subsequent determination of primary tumor site and stage. However, the primary site remains elusive in some patients even after an exhaustive examination. Human papillomavirus type 16 (HPV-16) is an important etiologic agent for HNSCCs that arise within the oropharynx but less so for tumors from nonoropharyngeal sites. Detection of HPV-16 or a surrogate marker may be useful in localizing tumor origin in patients who present with metastatic HNSCC. EXPERIMENTAL DESIGN We performed in situ hybridization (ISH) for HPV-16 on lymph node metastases from 68 patients with HNSCC. P16 immunohistochemistry was also performed because HPV-16 integration disrupts the retinoblastoma pathway and induces an overexpression of p16. RESULTS HPV-16 was detected in 22 of the 68 (32%) cases by ISH. When stratified by site of origin, HPV-16 was detected in 22 of 31 (71%) metastases from the oropharynx, but in none of the 37 (0%) metastases from other sites (P < 0.001; Fisher's exact). P16 expression was associated with the presence of HPV-16 by ISH: 21 of 22 HPV-16 positive tumors exhibited p16 expression, whereas only 4 of the 46 HPV-16-negative tumors were p16 positive (95% versus 9%; P < 0.001; Fisher's exact). P16 expression in the node metastases also correlated with site of tumor origin: 24 of 31 oropharyngeal tumors were p16 positive, whereas only 1 of 37 nonoropharyngeal tumors was p16 positive (77% versus 3%; P < 0.001; Fisher's exact). CONCLUSIONS For patients with metastatic HNSCC, detection of HPV-16 is a reliable way to establish origin from the oropharynx, either directly by ISH or indirectly by immunohistochemistry for p16 overexpression.
A domain-specific programming language for secure multiparty computation

We present a domain-specific programming language for Secure Multiparty Computation (SMC). Information is a resource of vital importance and considerable economic value to individuals, public administration, and private companies. This means that the confidentiality of information is crucial, but at the same time significant value can often be obtained by combining confidential information from various sources. This fundamental conflict between the benefits of confidentiality and the benefits of information sharing may be overcome using the cryptographic method of SMC where computations are performed on secret values and results are only revealed according to specific protocols We identify the key linguistic concepts of SMC and bridge the gap between high-level security requirements and low-level cryptographic operations constituting an SMC platform, thus improving the efficiency and security of SMC application development. The language is implemented in a prototype compiler that generates Java code exploiting a distributed cryptographic runtime.
Combining cognitive, semiotic and discourse analysis to explore the power of notations in visual programming

Using game design and programming to foster computational thinking acquisition has proved to be a successful strategy in recent years. In previous research with AgentSheets, we concluded that the semiotic richness of this visual programming environment, specifically designed to support computational thinking acquisition, could be explored more extensively to the benefit of learners. In particular, we realized that there are some additional representations of AgentSheets games and simulations that are not presented as programming tools in the interface, and yet they communicate new relevant meanings to the users. This paper reports on research where we artificially introduced such representations in a small follow-up experiment with selected participants from our previous research experiment. Our goal was to investigate the impact of such additional representations on program comprehension and modification tasks. To this end we contrasted empirical evidence of their performance in the two tasks with their verbal account of experience with AgentSheets. We used a combination of discourse analysis and inspections using Semiotic Engineering methods and the Cognitive Dimensions of Notations framework. Our findings go in two directions. First, we observed that additional representations have allowed participants to expand and correct previous learning. Therefore such representations can support new teaching strategies in computational thinking acquisition programs with AgentSheets. Second, we learned that the combination of methods we used to analyze empirical data - discourse analysis with semiotic and cognitive inspection techniques - can be used systematically in other research contexts, holding the promise of insightful results.
Improvements to GALA and dbERGE II: databases featuring genomic sequence alignment, annotation and experimental results

We describe improvements to two databases that give access to information on genomic sequence similarities, functional elements in DNA and experimental results that demonstrate those functions. GALA, the database of Genome ALignments and Annotations, is now a set of interlinked relational databases for five vertebrate species, human, chimpanzee, mouse, rat and chicken. For each species, GALA records pairwise and multiple sequence alignments, scores derived from those alignments that reflect the likelihood of being under purifying selection or being a regulatory element, and extensive annotations such as genes, gene expression patterns and transcription factor binding sites. The user interface supports simple and complex queries, including operations such as subtraction and intersections as well as clustering and finding elements in proximity to features. dbERGE II, the database of Experimental Results on Gene Expression, contains experimental data from a variety of functional assays. Both databases are now run on the DB2 database management system. Improved hardware and tuning has reduced response times and increased querying capacity, while simplified query interfaces will help direct new users through the querying process. Links are available at http://www.bx. psu.edu/.
Wellness Representation of Users in Social Media: Towards Joint Modelling of Heterogeneity and Temporality

The increasing popularity of social media has encouraged health consumers to share, explore, and validate health and wellness information on social networks, which provide a rich repository of Patient Generated Wellness Data (PGWD). While data-driven healthcare has attracted a lot of attention from academia and industry for improving care delivery through personalized healthcare, limited research has been done on harvesting and utilizing PGWD available on social networks. Recently, representation learning has been widely used in many applications to learn low-dimensional embedding of users. However, existing approaches for representation learning are not directly applicable to PGWD due to its domain nature as characterized by longitudinality, incompleteness, and sparsity of observed data as well as heterogeneity of the patient population. To tackle these problems, we propose an approach which directly learns the embedding from longitudinal data of users, instead of vector-based representation. In particular, we simultaneously learn a low-dimensional latent space as well as the temporal evolution of users in the wellness space. The proposed method takes into account two types of wellness prior knowledge: (1) temporal progression of wellness attributes; and (2) heterogeneity of wellness attributes in the patient population. Our approach scales well to large datasets using parallel stochastic gradient descent. We conduct extensive experiments to evaluate our framework at tackling three major tasks in wellness domain: attribute prediction, success prediction, and community detection. Experimental results on two real-world datasets demonstrate the ability of our approach in learning effective user representations.
Effects of Learning Styles on Learners' Preferences between PowerPoint and White/Chalkboard Lectures

®system. Previous research has found mixed results regarding whether students preferred PowerPoint or white/chalkboard to deliver class lectures. An explanation of the mixed results has not been clear. Although acknowledging the growing research that there was no evidence from experimental research to justify the need to assess learning styles in classrooms, we still questioned whether student learning styles might offer an explanation to the contradictory findings regarding preferences between PowerPoint and white/chalkboard presentations. No previous studies were found to have examined this possibility. The results supported a general preference for PowerPoint lectures to white/chalkboard lectures, but indicated no significant differences in preferences for the two lecture delivery methods based on the four learning styles. Nevertheless, the participants’ ratings and comments yielded useful information about what aspects of PowerPoint lectures they liked and disliked.
Neural Nets with Superlinear VC-Dimension

It has been known for quite a while that the Vapnik-Chervonenkis dimension (VC-dimension) of a feedforward neural net with linear threshold gates is at most O(w log w), where w is the total number of weights in the neural net. We show in this paper that this bound is in fact asymptotically optimal. More precisely, we exhibit for any depth d 3 a large class of feedforward neural nets of depth d with w weights that have VC-dimension (w log w). This lower bound holds even if the inputs are restricted to Boolean values. The proof of this result relies on a new method that allows us to encode more program-bits in the weights of a neural net than previously thought possible.
Molecular recognition as an information channel: The role of conformational changes

Molecular recognition, which is essential in processing information in biological systems, takes place in a crowded noisy biochemical environment and requires the recognition of a specific target within a background of various similar competing molecules. We consider molecular recognition as a transmission of information via a noisy channel and use this analogy to gain insights on the optimal, or fittest, molecular recognizer. We focus on the optimal structural properties of the molecules such as flexibility and conformation. We show that conformational changes upon binding, which often occur during molecular recognition, may optimize the detection performance of the recognizer. We thus suggest a generic design principle termed ‘conformational proofreading’ in which deformation enhances detection. We evaluate the optimal flexibility of the molecular recognizer, which is analogous to the stochasticity in a decision unit. In some scenarios, a flexible recognizer, i.e., a stochastic decision unit, performs better than a rigid, deterministic one. As a biological example, we discuss conformational changes during homologous recombination, the process of genetic exchange between two DNA strands.
Oncolytic virus therapy using genetically engineered herpes simplex viruses

An increasing number of oncolytic virus vectors has been developed lately for cancer therapy. Herpes simplex virus type 1 (HSV-1) vectors are particularly useful, because they can be genetically engineered to replicate and spread highly selectively in tumor cells and can also express multiple foreign transgenes. These vectors can manifest cytopathic effect in a wide variety of tumor types without damaging normal tissues, provide amplied gene delivery within the tumor, and induce specific antitumor immunity. Multiple recombinant HSV-1 vectors have been tested in patients with brain tumors and other cancers, which showed the feasibility of administering replication-competent HSV-1 vectors safely in human organs including the brain. Different approaches are currently undertaken to improve the efficacy of oncolytic HSV-1 therapy which include development of new generation vectors via further genetic engineering of existing safe vectors, combination with immune gene therapy, and combination with conventional therapies. Oncolytic virus therapy is a promising therapeutic modality that awaits establishing as an important treatment option for cancer patients in the near future.
Mutacins from Streptococcus mutans UA159 Are Active against Multiple Streptococcal Species

ABSTRACT Streptococcus mutans UA159, whose genome is completely sequenced, produces two nonlantibiotic mutacins, mutacin IV (encoded by nlmAB) and mutacin V (encoded by nlmC). In this study, we investigated the contribution of nlmA and nlmB to mutacin IV activity and demonstrated by performing genetic studies as well as by using semipurified molecules that, in contrast to a previous report, both of these genes are required for optimum mutacin IV activity. We also showed that mutacin IV is active against multiple Streptococcus species. In contrast, mutacin V displayed a narrower inhibitory range than mutacin IV. Our results suggest that mutacin IV and mutacin V may act synergistically to inhibit various organisms.
Understanding Gender and Domestic Violence From a Sample of Married Women in Urban Thailand

There is a widespread agreement among gender and family violence investigators that gender and socioeconomic inequalities play key roles in domestic violence against women (DVAW). By integrating the concepts of gender traditionalism and decision-making power into a variety of resource-based theories, this study develops a gender perspective to explore the linkages between gendered correlates and psychological and physical DVAW in urban Thailand. Based on a random sample of 770 married women in Bangkok, results from our Tobit regression models indicate that when Thai wives accept gender traditionalism, have significantly greater or smaller economic resources than their husbands, or have significantly greater or smaller decision-making power, they are at greater risk for multiple forms of domestic violence. However, contrary to expectations, Thai wives who report higher levels of social contact or integration do not experience less domestic violence. It is concluded that gender egalitarianism in urban Thailand can greatly reduce the risk of DVAW.
HUMAN SOCIAL ORGANIZATION, HUMAN DISEASE AND HUMAN SURVIVAL

It was Descartes, the 17th century philosopher and mathematician, who split spirit from matter, thought from material body. At the time this was an emtnently useful philosophic concept. As a result, investigation Into the organic functioning of man could thereafter be pursued with less chance of being caught up In the somewhat perilous quicksands of theology. The churchmen gradually came to rest reasonably content If the scientists restricted themselves to their own earthy business. Subsequent events in the succeeding centuries tend.ed to widen and preserve this dichotomy. Those aspects of human behaviour which would seem to distinguish man from other animal life, namely, the ability to think in abstract terms, to believe in ideologies, to feel compassion and SO on, were henceforward to be left to the theologiB.ns and the philosophers.
Treatment of chronic hepatitis C in patients with cirrhosis

Purpose of review This article reviews treatment options of the approved and soon-to-be approved direct-acting antivirals (DAA)-based therapies in individuals with hepatitis C virus (HCV) cirrhosis. Recent findings DAA-based therapies have been shown to be well tolerated and effective in achieving viral cure in individuals with compensated and decompensated cirrhosis. Preliminary studies suggest that viral eradication arrests fibrosis progression and could lead to fibrosis regression. Long-term benefits of successful HCV treatment in this population translate into less frequent hepatic decompensation and hepatocellular carcinoma development, improvements in liver disease severity, reduction of liver-related mortality, and potential obviation of the need for transplantation. The optimization of viral eradication rates requires longer duration therapy and/or more complex combinations of drugs, including ribavirin. Treatment decisions are guided by HCV genotype, renal function, drug–drug interactions, and the severity of cirrhosis. Safety concerns are paramount in individuals with advanced liver disease and continued vigilance for hepatotoxicity and other complications is warranted, especially in those with decompensated cirrhosis. Summary The availability of high potency DAA-based therapies with excellent safety profiles has transformed the HCV-infected cirrhotic population into a group that is no longer ‘difficult-to-treat’. Understanding the pretreatment factors that predict clinical benefits vs. harm remains key in treating this population.
A Parameterized Measure-and-Conquer Analysis for Finding a k-Leaf Spanning Treein an Undirected Graph

The problem of ﬁnding a spanning tree in an undirected graph with a maximum number of leaves is known to be NP -hard. We present an algorithm which ﬁnds a spanning tree with at least k leaves in time O ∗ (3 . 4575 k ) which improves the currently best algorithm. The estimation of the running time is done by using a non-standard measure. The present paper is one of the still few examples that employ the Measure & Conquer paradigm of algorithm analysis in the area of Parameterized Algorithmics.