Miracle-dz/UniFAR-FTUs huggingface dataset:
Non-Coding Keratin Variants Associate with Liver Fibrosis Progression in Patients with Hemochromatosis

Background Keratins 8 and 18 (K8/K18) are intermediate filament proteins that protect the liver from various forms of injury. Exonic K8/K18 variants associate with adverse outcome in acute liver failure and with liver fibrosis progression in patients with chronic hepatitis C infection or primary biliary cirrhosis. Given the association of K8/K18 variants with end-stage liver disease and progression in several chronic liver disorders, we studied the importance of keratin variants in patients with hemochromatosis. Methods The entire K8/K18 exonic regions were analyzed in 162 hemochromatosis patients carrying homozygous C282Y HFE (hemochromatosis gene) mutations. 234 liver-healthy subjects were used as controls. Exonic regions were PCR-amplified and analyzed using denaturing high-performance liquid chromatography and DNA sequencing. Previously-generated transgenic mice overexpressing K8 G62C were studied for their susceptibility to iron overload. Susceptibility to iron toxicity of primary hepatocytes that express K8 wild-type and G62C was also assessed. Results We identified amino-acid-altering keratin heterozygous variants in 10 of 162 hemochromatosis patients (6.2%) and non-coding heterozygous variants in 6 additional patients (3.7%). Two novel K8 variants (Q169E/R275W) were found. K8 R341H was the most common amino-acid altering variant (4 patients), and exclusively associated with an intronic KRT8 IVS7+10delC deletion. Intronic, but not amino-acid-altering variants associated with the development of liver fibrosis. In mice, or ex vivo, the K8 G62C variant did not affect iron-accumulation in response to iron-rich diet or the extent of iron-induced hepatocellular injury. Conclusion In patients with hemochromatosis, intronic but not exonic K8/K18 variants associate with liver fibrosis development.
Dose discrepancies between the Physicians' Desk Reference and the medical literature, and their possible role in the high incidence of dose-related adverse drug events.

BACKGROUND Adverse drug events (ADEs) are a major cause of morbidity and mortality, and even minor ADEs may adversely affect patients' compliance with treatment. Because most ADEs are dose-related phenomena, adjusting drug dosages to account for individual patients' needs and tolerances is fundamental to good therapeutics. OBJECTIVE To determine whether the Physicians' Desk Reference (PDR), the leading source of drug information for physicians, provides the full range of effective drug doses, especially the lowest, least ADE-prone doses of medications, for physicians to consider in treating patients. METHODS Review of dosage guidelines and dose-response information in the PDR. Comparison with dose-response data obtained from articles listed in MEDLINE from 1966 to 2000. RESULTS For many types of medications, physicians are frequently advised to use the lowest effective doses of drugs, especially initially. Yet, effective low doses determined in prerelease studies or in postrelease work are often omitted from the PDR, even when they have been recommended by expert panels. CONCLUSIONS Optimal therapeutics depends on the availability of comprehensive information. However, the PDR contains only the limited dose information from package inserts. Because the PDR was originally developed as a promotional device, there is no mechanism by which all clinically relevant dose-response data or important postrelease discoveries are regularly and rapidly incorporated into it. Thus, a gap exists in the availability of current and comprehensive dose information for physicians. This article provides information on lower, effective doses for 48 major medications, with an extensive reference list-a compilation of low-dose information not previously published, to our knowledge, in the medical literature. Physicians must have a readily accessible source of current and complete dose-response information to individualize drug therapy and minimize the risks of ADEs.
Image Digestion and Relevance Feedback in the ImageRover WWW Search Engine

Abstract ImageRover is a search by image content navigation tool for the world wide web. The staggering size of the WWW dictates certain strategies and algorithms for image collection, digestion, indexing, and user interface. This paper describes two key components of the ImageRover strategy: image digestion and relevance feedback. Image digestion occurs during image collection; robots digest the images they find, computing image decompositions and indices, and storing this extracted information in vector form for searches based on image content. Relevance feedback occurs during index search; users can iteratively guide the search through the selection of relevant examples. ImageRover employs a novel relevance feedback algorithm to determine the weighted combination of image similarity metrics appropriate for a particular query. ImageRover is available and running on the web site.
Web data extraction using the approach of segmentation and parsing

Given the URL's, automatically extracting the data from these result pages is very important for many applications, such as data integration, which need to cooperate with multiple web databases. In this paper we present a method which can extract the data of our interest out of the identified data regions, filter out the unwanted data records and finally put the extracted data into the table or export to csv files. Extraction procedure includes segmentation of contiguous as well as non contiguous data region, filtration of noise, and applying parsers. The implication of this is improved efficiency and better control over the extraction procedure. Our experimental results confirmed this.
Touch to Play -- Exploring Touch-Based Mobile Interaction with Public Displays

Mobile interactions with public displays are often indirect and not very convenient for multiple users at the same time. In this paper we use the physical, touch-based interaction with Near Field Communication (NFC) to investigate direct mobile interactions with public displays for multiple users. For that purpose, we adopt the Whack-a-Mole game for dynamic NFC-displays, which combine the physical interaction with NFC-tagged objects and the visual output capabilities of public displays. We show that a grid of NFC-tags can be used to implement direct mobile interaction with public displays in general and a highly interactive multiplayer game in particular. Our study shows that users appreciate this physical, NFC-based mobile interaction, although technical advances are still necessary in order to improve its recognition rate of about 70%. The study also indicates that users are willing to interact with large displays in public, but prefer private or semi-public places, where their interactions attract less attention.
Numerical solution of an integral equation for perpetual Bermudan options

We consider perpetual Bermudan options, which have no expiration and can be exercised every T time units. We use the Green's function approach to write down an integral equation for the value of a perpetual Bermudan call option on an expiration date; this integral equation leads to a Wiener–Hopf problem. We discretize the integral in the integral equation to convert the problem to a linear algebra problem, which is straightforward to solve, and this enables us to find the location of the free boundary and the value of the perpetual Bermudan call. We compare our results to earlier studies which used other numerical methods.
Robotic ultrasound trajectory planning for volume of interest coverage

Medical robotic ultrasound offers potential to assist interventions, ease long-term monitoring and reduce operator dependency. Various techniques for remote control of ultrasound probes through telemanipulation systems have been presented in the past, however not exploiting the potential of fully autonomous acquisitions directly performed by robotic systems. In this paper, a trajectory planning algorithm for automatic robotic ultrasound acquisition under expert supervision is introduced. The objective is to compute a suitable path for covering a volume of interest selected in diagnostic images, for example by prior segmentation. A 3D patient surface point cloud is acquired using a depth camera, which is the sole prerequisite besides the volume delineation. An easily parameterizable path function generates single or multiple parallel scan trajectories capable of dealing with large target volumes. A spline is generated through the preliminary path points and is transferred to a lightweight robot to perform the ultrasound scan using an impedance control mode. The proposed approach is validated via simulation as well as on phantoms and on animal viscera.
Effects of Black Pepper (Piper Nigrum), Turmeric Powder (Curcuma Longa) and Coriander Seeds (Coriandrum Sativum) and Their Combinations as Feed Additives on Growth Performance, Carcass Traits, Some Blood Parameters and Humoral Immune Response of Broiler Chickens

Different herbs and spices have been used as feed additives for various purposes in poultry production. This study was conducted to assess the effect of feed supplemented with black pepper (Piper nigrum), turmeric powder (Curcuma longa), coriander seeds (Coriandrum sativum) and their combinations on the performance of broilers. A total of 210 (Cobb) one-d-old chicks were divided into seven groups of 30 birds each. The treatments were: a control group received no supplement, 0.5% black pepper (T1), 0.5% turmeric powder (T2), 2% coriander seeds (T3), a mixture of 0.5% black pepper and 0.5% turmeric powder (T4), a mixture of 0.5% black pepper and 2% coriander seed (T5), and a mixture of 0.5% black pepper, 0.5% turmeric powder and 2% coriander seeds (T6). Higher significant values of body weight gain during the whole period of 5 weeks (p<0.001) were observed in broilers on T1, T3, T5, and T6 compared to control. Dietary supplements with T1, T2, T3, and T6 improved the cumulative G:F of broilers during the whole period of 5 weeks (p<0.001) compared with control. The dressing percentage and edible giblets were not influenced by dietary supplements, while higher values of relative weight of the liver (p<0.05) were obtained in T5 and T6 compared to control. The addition of feed supplements in T5 and T6 significantly increased serum total protein and decreased serum glucose, triglycerides and alkaline phosphatase concentrations compared with the control group (p<0.05). Broilers on T6 showed significant decrease in the serum glutamate pyruvate transaminase concentration (p<0.05) compared to control. The broilers having T5 and T6 supplemented feed had relatively greater antibody titre (p<0.001) at 35 d of age than control. It is concluded that dietary supplements with black pepper or coriander seeds or their combinations enhanced the performance and health status of broiler chickens.
Popular Culture as Oppositional Culture: Rap as Resistance

Bonnie Mitchell and Joe Feagin (1995) build on the theory of oppositional culture, arguing that African Americans, American Indians, and Mexican Americans draw on their own cultural resources to resist oppression under internal colonialism. In this paper, rap music is identified as an important African American popular cultural form that also emerges as a form of oppositional culture. A brief analysis of the lyrics of political and gangsta rappers of the late 1980s and early 1990s, provides key themes of distrust, anger, resistance, and critique of a perceived racist and discriminatory society. Rap music is discussed as music with a message of resistance, empowerment, and social critique, and as a herald of the Los Angeles riots of 1992.
Efficient automatic search query formulation using phrase‐level analysis

Over the past decade, the volume of information available digitally over the Internet has grown enormously. Technical developments in the area of search, such as Google's Page Rank algorithm, have proved so good at serving relevant results that Internet search has become integrated into daily human activity. One can endlessly explore topics of interest simply by querying and reading through the resulting links. Yet, although search engines are well known for providing relevant results based on users' queries, users do not always receive the results they are looking for. Google's Director of Research describes clickstream evidence of frustrated users repeatedly reformulating queries and searching through page after page of results. Given the general quality of search engine results, one must consider the possibility that the frustrated user's query is not effective; that is, it does not describe the essence of the user's interest. Indeed, extensive research into human search behavior has found that humans are not very effective at formulating good search queries that describe what they are interested in. Ideally, the user should simply point to a portion of text that sparked the user's interest, and a system should automatically formulate a search query that captures the essence of the text. In this paper, we describe an implemented system that provides this capability. We first describe how our work differs from existing work in automatic query formulation, and propose a new method for improved quantification of the relevance of candidate search terms drawn from input text using phrase‐level analysis. We then propose an implementable method designed to provide relevant queries based on a user's text input. We demonstrate the quality of our results and performance of our system through experimental studies. Our results demonstrate that our system produces relevant search terms with roughly two‐thirds precision and recall compared to search terms selected by experts, and that typical users find significantly more relevant results (31% more relevant) more quickly (64% faster) using our system than self‐formulated search queries. Further, we show that our implementation can scale to request loads of up to 10 requests per second within current online responsiveness expectations (<2‐second response times at the highest loads tested).
On the Sound-System of Central Algonquian

1. The Central Algonquian Languages form a group which, together with Eastern Algonquian, constitutes the Eastern-Central branch of the Algonquian stock. While the similarity between the Central Algonquian languages is evident, the exact grouping is doubtful. Michelson (BAE, Ann. Rep. 28, 221) classifies them as follows: (1) Cree group: a number of dialects falling into two general types, Cree and Montagnais, (2) Menomini, a single dialect, (3) Sauk group: Sauk, Fox, Kickapoo, and the somewhat divergent Shawnee, (4) Ojibwa group: a number of dialects known as Ojibwa (Chippewa), Algonquin, Ottawa, Potawatomi, (5) Peoria group: Peoria, Miami, Illinois, (6) Delaware group, (7) Natick group. The following notes aim to show the chief correspondences between the first four groups. It is hoped that the outline here given may serve as a basis for further discussion. '
Systematic Evaluation of the Cellular Innate Immune Response During the Process of Human Atherosclerosis

Background The concept of innate immunity is well recognized within the spectrum of atherosclerosis, which is primarily dictated by macrophages. Although current insights to this process are largely based on murine models, there are fundamental differences in the atherosclerotic microenvironment and associated inflammatory response relative to humans. In this light, we characterized the cellular aspects of innate immune response in normal, nonprogressive, and progressive human atherosclerotic plaques. Methods and Results A systematic analysis of innate immune response was performed on 110 well‐characterized human perirenal aortic plaques with immunostaining for specific macrophage subtypes (M1 and M2 lineage) and their activation markers, neopterin and human leukocyte antigen–antigen D related (HLA‐DR), together with dendritic cells (DCs), natural killer (NK) cells, mast cells, neutrophils, and eosinophils. Normal aortae were devoid of low‐density lipoprotein, macrophages, DCs, NK cells, mast cells, eosinophils, and neutrophils. Early, atherosclerotic lesions exhibited heterogeneous populations of (CD68+) macrophages, whereby 25% were double positive “M1” (CD68+/ inducible nitric oxide synthase [iNOS]+/CD163−), 13% “M2” double positive (CD68+/iNOS −/CD163+), and 17% triple positive for (M1) iNOS (M2)/CD163 and CD68, with the remaining (≈40%) only stained for CD68. Progressive fibroatheromatous lesions, including vulnerable plaques, showed increasing numbers of NK cells and fascin‐positive cells mainly localized to the media and adventitia whereas the M1/M2 ratio and level of macrophage activation (HLA‐DR and neopterin) remained unchanged. On the contrary, stabilized (fibrotic) plaques showed a marked reduction in macrophages and cell activation with a concomitant decrease in NK cells, DCs, and neutrophils. Conclusions Macrophage “M1” and “M2” subsets, together with fascin‐positive DCs, are strongly associated with progressive and vulnerable atherosclerotic disease of human aorta. The observations here support a more complex theory of macrophage heterogeneity than the existing paradigm predicated on murine data and further indicate the involvement of (poorly defined) macrophage subtypes or greater dynamic range of macrophage plasticity than previously considered.
Non-Transferable Utility Coalitional Games via Mixed-Integer Linear Constraints

Coalitional games serve the purpose of modeling payoff distribution problems in scenarios where agents can collaborate by forming coalitions in order to obtain higher worths than by acting in isolation. In the classical Transferable Utility (TU) setting, coalition worths can be freely distributed amongst agents. However, in several application scenarios, this is not the case and the Non-Transferable Utility setting (NTU) must be considered, where additional application-oriented constraints are imposed on the possible worth distributions. In this paper, an approach to define NTU games is proposed which is based on describing allowed distributions via a set of mixed-integer linear constraints applied to an underlying TU game. It is shown that such games allow non-transferable conditions on worth distributions to be specified in a natural and succinct way. The properties and the relationships among the most prominent solution concepts for NTU games that hold when they are applied on (mixed-integer) constrained games are investigated. Finally, a thorough analysis is carried out to assess the impact of issuing constraints on the computational complexity of some of these solution concepts.
Mining succinct and high-coverage API usage patterns from source code

During software development, a developer often needs to discover specific usage patterns of Application Programming Interface (API) methods. However, these usage patterns are often not well documented. To help developers to get such usage patterns, there are approaches proposed to mine client code of the API methods. However, they lack metrics to measure the quality of the mined usage patterns, and the API usage patterns mined by the existing approaches tend to be many and redundant, posing significant barriers for being practical adoption. To address these issues, in this paper, we propose two quality metrics (succinctness and coverage) for mined usage patterns, and further propose a novel approach called Usage Pattern Miner (UP-Miner) that mines succinct and high-coverage usage patterns of API methods from source code. We have evaluated our approach on a large-scale Microsoft codebase. The results show that our approach is effective and outperforms an existing representative approach MAPO. The user studies conducted with Microsoft developers confirm the usefulness of the proposed approach in practice.
MANCaLog: a logic for multi-attribute network cascades

The modeling of cascade processes in multi-agent systems in the form of complex networks has in recent years become an important topic of study due to its many applications: the adoption of commercial products, spread of disease, the diffusion of an idea, etc. In this paper, we begin by identifying a desiderata of seven properties that a framework for modeling such processes should satisfy: the ability to represent attributes of both nodes and edges, an explicit representation of time, the ability to represent non-Markovian temporal relationships, representation of uncertain information, the ability to represent competing cascades, allowance of non-monotonic diffusion, and computational tractability. We then present the MANCaLog language, a formalism based on logic programming that satisfies all these desiderata, and focus on algorithms for finding minimal models (from which the outcome of cascades can be obtained) as well as how this formalism can be applied in real world scenarios. We are not aware of any other formalism in the literature that meets all of the above requirements.
Improved Asymptotic Capacity Lower Bound for OFDM System with Compressed Sensing Channel Estimation for Bernoulli Gaussian Channel

We propose an improved capacity lower bound for OFDM system with compressed sensing channel estima- tion for Bernoulli-Gaussian channel. We improve the known capacity lower bound which is based on Lasso compressed sensing channel estimation, by replacing the Lasso based estimate with an MMSE estimate, known to be optimal in the MMSE sense and achievable with practical algorithms for a broad range of system parameters setup. Additionally, for the system with equi-powered pilot subcarriers we opti- mize the capacity lower bound byfinding the optimal average fraction of pilot subcarriers used for channel estimation and optimal pilot to data power ratio given the average symbol powerpersubcarrier,andproposeanoptimizationprocedure with polynomial complexity.
Between a Rock and a Hard Place: Shia Ismaili Muslim Girls Negotiate Islam in the Classroom

ABSTRACT This case study investigates the experiences of Shia Ismaili Muslim girls as they encounter themselves as subjects of social studies curriculums on Islam. A postcolonial lens is used to examine differently empowered subjectivities and curricular epistimes within the high school world history context. In an effort to understand their experiences, this study focuses on how the students position themselves in relation to the curriculum, and ultimately asks, to what extent do students from minority communities of interpretation appropriate or resist the authoritative narrative of Islam offered in their classrooms, particularly around the question, “Who is a Muslim? ” The central finding revealed a paradox of representation and participation for these students, who found their practice and interpretation of Islam silenced in the classroom curriculum, and yet felt obliged to defend Islam and educate others against stereotypes of Muslims. The implications of this study compel educators to explore decolonial approaches to teaching about the religious other.