Miracle-dz/UniFAR-FTUs huggingface dataset:
Mapping Yeast Transcriptional Networks

The term “transcriptional network” refers to the mechanism(s) that underlies coordinated expression of genes, typically involving transcription factors (TFs) binding to the promoters of multiple genes, and individual genes controlled by multiple TFs. A multitude of studies in the last two decades have aimed to map and characterize transcriptional networks in the yeast Saccharomyces cerevisiae. We review the methodologies and accomplishments of these studies, as well as challenges we now face. For most yeast TFs, data have been collected on their sequence preferences, in vivo promoter occupancy, and gene expression profiles in deletion mutants. These systematic studies have led to the identification of new regulators of numerous cellular functions and shed light on the overall organization of yeast gene regulation. However, many yeast TFs appear to be inactive under standard laboratory growth conditions, and many of the available data were collected using techniques that have since been improved. Perhaps as a consequence, comprehensive and accurate mapping among TF sequence preferences, promoter binding, and gene expression remains an open challenge. We propose that the time is ripe for renewed systematic efforts toward a complete mapping of yeast transcriptional regulatory mechanisms.
Implementing domain-specific languages as the foundation of an honors intro CS course

This position paper describes an honors introductory Computer Science course focused on designing and implementing domain-specific programming languages. The course presents programming language design as a fundamental tool for software engineering. Students build languages for prototypes of several nontrivial products (such as PowerPoint and TurboTax). The course aims to convey fundamental ideas behind programming languages in a form that mainstream Computer Science students can appreciate early in their careers. The paper includes descriptions of and links to assignments and course materials.
Research on project portfolio selection and decision-making process based on Lotka-Volterra model

Based on Lotka-Volterra model, a congener competitive project portfolio selection model with project inter-relationships is built up. To simplify the project portfolio decision-making, an improved decision-making process under LVPPS model is proposed and described specifically through an example. Project portfolio selection and scale decision are included in the same analytical framework.
Community and School-Based Health Education for Dengue Control in Rural Cambodia: A Process Evaluation

Dengue fever continues to be a major public health problem in Cambodia, with significant impact on children. Health education is a major means for prevention and control of the National Dengue Control Program (NDCP), and is delivered to communities and in schools. Drawing on data collected in 2003–2004 as part of an ethnographic study conducted in eastern Cambodia, we explore the approaches used in health education and their effectiveness to control dengue. Community health education is provided through health centre outreach activities and campaigns of the NDCP, but is not systematically evaluated, is under-funded and delivered irregularly; school-based education is restricted in terms of time and lacks follow-up in terms of practical activities for prevention and control. As a result, adherence is partial. We suggest the need for sustained routine education for dengue prevention and control, and the need for approaches to ensure the translation of knowledge into practice.
Trends, major medical complications, and charges associated with surgery for lumbar spinal stenosis in older adults.

CONTEXT In recent decades, the fastest growth in lumbar surgery occurred in older patients with spinal stenosis. Trials indicate that for selected patients, decompressive surgery offers an advantage over nonoperative treatment, but surgeons often recommend more invasive fusion procedures. Comorbidity is common in older patients, so benefits and risks must be carefully weighed in the choice of surgical procedure. OBJECTIVE To examine trends in use of different types of stenosis operations and the association of complications and resource use with surgical complexity. DESIGN, SETTING, AND PATIENTS Retrospective cohort analysis of Medicare claims for 2002-2007, focusing on 2007 to assess complications and resource use in US hospitals. Operations for Medicare recipients undergoing surgery for lumbar stenosis (n = 32,152 in the first 11 months of 2007) were grouped into 3 gradations of invasiveness: decompression alone, simple fusion (1 or 2 disk levels, single surgical approach), or complex fusion (more than 2 disk levels or combined anterior and posterior approach). MAIN OUTCOME MEASURES Rates of the 3 types of surgery, major complications, postoperative mortality, and resource use. RESULTS Overall, surgical rates declined slightly from 2002-2007, but the rate of complex fusion procedures increased 15-fold, from 1.3 to 19.9 per 100,000 beneficiaries. Life-threatening complications increased with increasing surgical invasiveness, from 2.3% among patients having decompression alone to 5.6% among those having complex fusions. After adjustment for age, comorbidity, previous spine surgery, and other features, the odds ratio (OR) of life-threatening complications for complex fusion compared with decompression alone was 2.95 (95% confidence interval [CI], 2.50-3.49). A similar pattern was observed for rehospitalization within 30 days, which occurred for 7.8% of patients undergoing decompression and 13.0% having a complex fusion (adjusted OR, 1.94; 95% CI, 1.74-2.17). Adjusted mean hospital charges for complex fusion procedures were US $80,888 compared with US $23,724 for decompression alone. CONCLUSIONS Among Medicare recipients, between 2002 and 2007, the frequency of complex fusion procedures for spinal stenosis increased while the frequency of decompression surgery and simple fusions decreased. In 2007, compared with decompression, simple fusion and complex fusion were associated with increased risk of major complications, 30-day mortality, and resource use.
Implementation of Dynamic Evolution Control of Bidirectional DC–DC Converter for Interfacing Ultracapacitor Energy Storage to Fuel-Cell System

An electric vehicle powered by fuel cells (FCs) gives far more promising performance. An FC is a clean energy source and has a high energy-storage capability. However, an FC has a slow dynamic response. A secondary power source is needed during start-up and transient conditions. An ultracapacitor can be used as a secondary power source to improve the performance and efficiency of the overall system. Several methods have been devised to connect an energy-storage device to an FC. This paper presents a converter system for connecting an ultracapacitor as secondary energy storage to an FC electric-vehicle system. A bidirectional dc-dc converter is used for interfacing ultracapacitor energy storage to an FC system. The controller of the converter system was designed and implemented based on dynamic evolution control. The performance of the proposed dynamic evolution control is tested through simulation and experiment. Simulation and experimental results show that the proposed techniques are suitable for controlling bidirectional dc-dc converters.
A Novel Circular Ring Histogram for Content-Based Image Retrieval

This paper presents a novel histogram-based image Retrieval method called the Circular Ring Histogram (CRH). The CRH utilizes groups of circular rings to segment the image firstly and then build the color histogram over these rings. It is robust to the image rotation and scaling. The way to build the histogram integrates the spatial information into histogram. The experimental results demonstrate the feasibility and efficiency of our proposed scheme.
Analyzing Evolution Strategy via Stochastic Approximation Methods

The main objective of this paper is to analyze the evolution strategy by use of stochastic approximation methods Both constant and decreasing step size algorithms are studied Convergence and estimation error bounds for the evolution strategy are developed First the algorithm is converted to a recursively de ned scheme of stochastic approximation type Then the analysis is carried out by using the analytic tools from stochastic approximation In lieu of examining the discrete iterates suitably scaled sequences are de ned These interpolated sequences are then studied in detail It is shown that the limits of the sequences have natural connection to certain continuous time dynamical systems
A Theoretical Study on Clothing Conformity: Conformity type, Reference Group, and Influencing factor

As a preliminary work for the clothing conformity study, Its theoretical backgrounds were reviewed. In the view of convertibility into clothing conformity, two prevailing conformity types were studied. One is normative-social influence and informational-social influence classified by Deutsch and Gerald. And the other is Kelman's classification which includes compliance, identification and internalization. Reference group, as an object of conformity, was studied. In addition to Engel and Blackwell' s and Assael's classification, the reference groups which were revealed in the studies of consumer behavior and clothing behavior were reviewed. The factors were reviewed which influence conformity and clothing conformity. They were product factor, group factor, situational factor and individual factor.
A Novel Motion Based Lip Feature Extraction for Lip-Reading

In a lip-reading system, one key issue is how to extract the visual features, which greatly impact on the lip-reading recognition accuracy and efficiency. In this paper, we propose a novel motion based visual feature representation. Compared with the existing methods, our approach focuses on the crucial part of lip movement, but not all pixels around lip contours for different utterance, and captures the motion tracks of each part. Accordingly, distinctive feature vectors are built to represent the whole lip motion process for the specified utterance, rather than the separate frame images. Experimental result shows the efficacy of the proposed approach.
Urban Revival in America, 2000 to 2010

This paper documents and explains the striking rise in the proclivity of college-educated individuals to reside near city centers since 2000. We show that this recent urban revival is driven almost entirely by younger college graduates in larger cities. With a residential choice model, we quantify the role of jobs, amenities, and house prices in explaining this trend. We find that the rising taste of young college graduates for non-tradable service amenities like restaurants and nightlife accounts for more than 40 percent of their movement toward city centers. Complementary data shows a corresponding rise in young college graduate expenditures on and trips to non-tradable services. We then link changes in both consumption and urbanization to secular trends of top income growth and delayed family formation amongst young college graduates.
Vitamin D and chronic kidney disease

Chronic kidney disease (CKD) has been recognized as a significant global health problem because of the increased risk of total and cardiovascular morbidity and mortality. Vitamin D deficiency or insufficiency is common in patients with CKD, and serum levels of vitamin D appear to have an inverse correlation with kidney function. Growing evidence has indicated that vitamin D deficiency may contribute to deteriorating renal function, as well as increased morbidity and mortality in patients with CKD. Recent studies have suggested that treatment with active vitamin D or its analogues can ameliorate renal injury by reducing fibrosis, apoptosis, and inflammation in animal models; this treatment also decreases proteinuria and mortality in patients with CKD. These renoprotective effects of vitamin D treatment are far beyond its classical role in the maintenance of bone and mineral metabolism, in addition to its pleiotropic effects on extra-mineral metabolism. In this review, we discuss the altered metabolism of vitamin D in kidney disease, and the potential renoprotective mechanisms of vitamin D in experimental and clinical studies. In addition, issues regarding the effects of vitamin D treatment on clinical outcomes are discussed.
Saturation and Thermalization of the Magnetorotational Instability: Recurrent Channel Flows and Reconnections

The nonlinear evolution and saturation mechanism of the magnetorotational instability (MRI) are investigated using three-dimensional resistive MHD simulations. A local shearing box is used for our numerical analysis, and the simulations begin with a purely vertical magnetic field. We find that the magnetic stress in the nonlinear stage of the MRI is strongly fluctuating. The time evolution shows the quasi-periodic recurrence of spike-shaped variations, typically for a few orbits, which correspond to the rapid amplification of the magnetic field by the nonlinear growth of a two-channel solution followed by decay through magnetic reconnections. The increase rate of the total energy in the shearing box system is analytically related to the volume-averaged torque in the system. We find that at the saturated state this energy gain of the system is balanced with the increase of thermal energy, mostly due to joule heating. The spike-shaped time evolution is a general feature of the nonlinear evolution of the MRI in disks threaded by vertical fields and can be seen if the effective magnetic Reynolds number is larger than about unity.
Mercury's Atmosphere from Mariner 10: Preliminary Results

Analysis of data obtained by the ultraviolet experiment on Mariner 10 indicates that Mercury is surrounded by a thin atmosphere consisting in part of helium. The partial pressure of helium at the terminator is about 5 x 10-12 millibar. The total surface pressure of the atmosphere is less than about 2 x 10-9 millibar. Upper limits are set for the abundance of various gases, including hydrogen, oxygen, carbon, argon, neon, and xenon. The wavelength dependence of Mercury's surface albedo is similar to that of the moon over a broad range of wavelengths from 500 to 1600 angstroms. Strong signals were recorded by the airglow instrument as Mariner 10 passed through the cavity behind Mercury. They are as yet unexplained but may provide information on the properties of the local plasma.
Semantic Interpretation of Structured Log Files

Data from computer log files record traces of events involving user activity, applications, system software and network traffic. Logs are usually intended for diagnostic and debugging purposes, but their data can be extremely useful in system audits and forensic investigations. Logs created by intrusion detection systems, Web servers, antivirus and anti-malware systems, firewalls and network devices have information that can reconstruct the activities of malware or a malicious agent, help plan for remediation and prevent attacks by revealing probes or intrusions before damage has been done. While existing tools like Splunk can help analyze logs with known schemas, understanding log whose format is unfamiliar or associated with new device or custom application can be challenging. We describe a framework for analyzing logs and automatically generating a semantic description of their schema and content in RDF. The framework begins by normalizing the log into columns and rows using regular expression-based and dictionary-based classifiers. Leveraging our existing work on inferring the semantics of tables, we associate semantic types with columns and, when possible, map them to concepts in general knowledge-bases (e.g. DBpedia) and domain specific ones (e.g., Unified Cybersecurity Ontology). We link cell values to known type instances (e.g., an IP address) and suggest relationships between columns. Converting large and verbose log files into such semantic representations reveals their meaning and supports search, integration and reasoning over the data.
Bone marrow transplantation for acute leukemia.

Between May 1976 and December 1983, 200 patients underwent bone marrow transplantation (BM1) for hematologic malignancies at our center; 164 had acute leukemia. After administration of high dose radiochemotherapy for marrow ablation and immunosuppression, these 164 patients received marrow grafts from histocompatible sibling donors. Graft-versus-host disease prophylaxis (and therapy) consisted of either methotrexate and prednisone or cyc1osporin A and prednisone. All patients have been followed for a minimum of 3 months after BMT. Results are summarized in Table 1 and Fig. 1.
Improve the Output from a MCQ Test Item Generator Using Statistical NLP

In this study I use statistical Natural Language Processing and adapted Controlled Language methods to preprocess individual documents before they are used as source documents for a system which automatically generates MCQ (Multiple Choice Question) test items. The literature observes that Natural Language Generation system evaluation is nontrivial and so the success of the featured methods is evaluated using a process suited to the featured domain. Generated MCQ test items are combined with items that have been created using traditional methods and then a routine is selected by a domain expert. The results provide some evidence to support the incorporation of some of the featured methods into future versions of the software.
An Evaluation Framework for Privacy-Preserving Record Linkage

Privacy-preserving record linkage (PPRL) addresses the problem of identifying matching records from different databases that correspond to the same real-world entities using quasi-identifying attributes (in the absence of unique entity identifiers), while preserving privacy of these entities. Privacy is being preserved by not revealing any information that could be used to infer the actual values about the records that are not reconciled to the same entity (non-matches), and any confidential or sensitive information (that is not agreed upon by the data custodians) about the records that were reconciled to the same entity (matches) during or after the linkage process. The PPRL process often involves three main challenges, which are scalability to large databases, high linkage quality in the presence of data quality errors, and sufficient privacy guarantees. While many solutions have been developed for the PPRL problem over the past two decades, an evaluation and comparison framework of PPRL solutions with standard numerical measures defined for all three properties (scalability, linkage quality, and privacy) of PPRL has so far not been presented in the literature. We propose a general framework with normalized measures to practically evaluate and compare PPRL solutions in the face of linkage attack methods that are based on an external global dataset. We conducted experiments of several existing PPRL solutions on real-world databases using our proposed evaluation framework, and the results show that our framework provides an extensive and comparative evaluation of PPRL solutions in terms of the three properties.
OR Practice - Efficient Short-Term Allocation and Reallocation of Patients to Floors of a Hospital During Demand Surges

Many hospitals face the problem of insufficient capacity to meet demand for inpatient beds, especially during demand surges. This results in quality degradation of patient care due to large delays from admission time to the hospital until arrival at a floor. In addition, there is loss of revenue because of the inability to provide service to potential patients. A solution to the problem is to proactively transfer patients between floors in anticipation of a demand surge. Optimal reallocation poses an extraordinarily complex problem that can be modeled as a finite-horizon Markov decision process. Based on the optimization model, a decision-support system has been developed and implemented at Windham Hospital in Willimantic, Connecticut. Projections from an initial trial period indicate very significant financial gains of about 1% of their total revenue, with no negative impact on any standard quality of care or staffing effectiveness indicators. In addition, the hospital showed a marked improvement in quality of care because of a resulting decrease of almost 50% in the average time that an admitted patient has to wait from admission until being transferred to a floor.
Molecular Heterogeneity of Photosystem I (psaD, psaE, psaF, psaH, and psaL Are All Present in Isoforms in Nicotiana spp.)

The protein composition of photosystem I (PSI) was examined in Nicotiana spp. by high-resolution polyacrylamide gel electrophoresis, N-terminal amino acid sequencing, and immunoblot analysis. Five PSI proteins show polymorphism in an amphidiploid species, Nicotiana tabacum, but not in its ancestral diploid species, Nicotiana sylvestris and Nicotiana tomentosiformis. These Nicotiana spp. appear to have at least 18 PSI proteins per genome that range in molecular mass from 3 to 20 kD. They include the products of nuclear genes psaD, psaE, psaF, psaG, psaH, psaK, and psaL, the product of chloroplast gene psaC, N-terminally blocked proteins of 4.5 and 3.0 kD, and an unidentified protein of 12.5 kD. The psaD, psaF, psaH, and psaL products have two isoforms each that are distinguished by different mobilities in polyacrylamide gel electrophoresis, and the psaE product has four isoforms. The two isoforms of the psaD product have distinct amino acid sequences, indicating that they are encoded by different genes within the genome. Four isoforms of the psaE products can be classified into two groups by N-terminal amino acid sequence, indicating that at least two psaE genes are present in the genome. To examine whether the polymorphic nature of PSI is peculiar to Nicotiana spp. , we carried out immunoblot analysis of the psaD and psaE products in isogenic lines of tomato (Lycopersicon esculentum), Arabidopsis thaliana, red bean (Vigna angularis), and corn (Zea mays). Two electrophoretically distinct isoforms were found for the psaD products of tomato, A. thaliana, and corn, and two isoforms of psaE products were detected in tomato, A. thaliana, and red bean. These results suggest that the nuclear-encoded subunits of PSI, except for the psaG and psaK products, generally have two isoforms.