Miracle-dz/UniFAR-FTUs huggingface dataset:
The design and analysis of cohort studies

This book complements the first volume in the series, on case-control studies, and the two together provide a comprehensive account of the analysis of the major types of study in cancer epidemiology. In addition, this volume has a chapter on study design, covering both the case-control and cohort approach. The scope ranges from an account of the elementary and descriptive approaches to cohort analysis to the fitting of regression models for incidence rates with general risk functions. Particular attention is given to the use of a case-control approach embedded in a cohort study. As in the first volume, all the methods described are illustrated by examples from real studies, and the data from these studies are provided in appendices to enable the reader to go through the computations themselves. The book is intended for the medical epidemiologist with an interest in the quantitative aspects of the subject, and the statistician who is looking for a reasonably complete development of the statistical concepts and methods in current use in this area of epidemiology, as well as medical epidemiologists; statisticians; oncologists; students in biostatistics and related fields.
Computer methods to locate signals in nucleic acid sequences

This paper describes computer methods for locating signals in nucleic acid sequences. The signals include ribosome binding sites, promoter sequences and splice junctions. The methods are of use both to those trying to interpret the function of newly determined sequences and to those studying the molecular mechanisms involved in the recognition of these special signal sequences.
BIOLOG - a DNA sequence analysis system in PROLOG

BIOLOG contains facilities for the analysis of nucleic acid sequences. These facilities are available through queries and commands of the underlying implementation language PROLOG. Familiarity with PROLOG is gained by using the built-in BIOLOG functions. This experience should enable the user to extend the current system and define new facilities.
Exploring social network interactions in enterprise systems: the role of virtual co‐presence

This paper investigates the impact of social media interactions on the use context of enterprise systems (ES) at a global telecommunications company based in Europe. We conducted a detailed field study of users in three countries who execute tasks collectively using social media capabilities within their ES. The findings provide rich insights into these social media interactions, their influence on ES users' sense of ‘presence’ and their impact on the completion of tasks. Our key research contribution is to introduce the idea of ‘virtual co‐presence’ as a means of understanding the digitally mediated presence of ES users. In addition, we demonstrate how virtual co‐presence and the relationships afforded by social media shape ES users' interactions and collective completion of tasks in a dispersed work context. Drawing on the insights gained from the effect of virtual co‐presence on ES users, the paper outlines some implications for the theory and practice of collective work in ES use.
The many faces of information technology interruptions: a taxonomy and preliminary investigation of their performance effects

Despite the growing importance of information technology (IT) interruptions for individual work, very little is known about their nature and consequences. This paper develops a taxonomy that classifies interruptions based on the relevance and structure of their content, and propositions that relate different interruption types to individual performance. A qualitative approach combining the use of log diaries of professional workers and semi‐structured interviews with product development workers provide a preliminary validation of the taxonomy and propositions and allow for the discovery of a continuum of interruption events that fall in‐between the extreme types in the taxonomy. The results show that some IT interruptions have positive effects on individual performance, whilst others have negative effects, or both. The taxonomy developed in the paper allows for a better understanding of the nature of different types of IT interruption and their consequences on individual work. By showing that different types of interruptions have different effects, the paper helps to explain and shed light on the inconsistent results of past research.
Introduction to the special issue on ‘dark side of information technology use’ – part two

*Department of Management Science, Lancaster University (Management School), Rm A42, Bailrigg, Lancaster, UK, email: m.tarafdar@lancaster.ac. uk, Analytics and Information Systems Management, College of Business, University of Tennessee Chattanooga, Fletcher 406-C, 615 McCallie Ave, Chattanooga, TN 37403, USA, email: Gupta@utc.edu and Information Systems and Decision Sciences, Mihaylo School of Business and Economics, California State University, Fullerton, Room SGMH-4160, 800 N. State College Blvd., Fullerton, CA 92834, USA, email: oturel@fullerton.edu
S1-sensitive sites in the supercoiled double-stranded form of tomato golden mosaic virus DNA component B: identification of regions of potential alternative secondary structure and regulatory function

The sensitivity of the supercoiled double-stranded form of the DNA of tomato golden mosaic virus (TGMV), a geminivirus, to the single-strand specific enzyme S1 nuclease has been demonstrated. Specific S1 cleavage sites were identified in TGMV DNA component B by cloning into the single-strand bacteriophage vector M13 mp8 and sequencing of the inserted DNA. Analysis of the DNA sequence at the sites of S1 sensitivity in TGMV DNA component B revealed several possible regions of alternative secondary structure which were clustered in an intergenic region upstream of the starts of the two major open reading frames which are in opposite orientations. This region contains putative transcriptional promoter and modulatory sequences and a possible replication origin. The extreme S1 sensitivity of the supercoiled form of TGMV DNA component A precluded its cloning under the conditions employed for selective cleavage of DNA component B.
Efficient octopine Ti plasmid-derived vectors for Agrobacterium- mediated gene transfer to plants

A two-component cloning system to transfer foreign DNA into plants was derived from the octopine Ti plasmid pTiB6S3. pGV2260 is a non-oncogenic Ti plasmid from which the T-region is deleted and substituted by pBR322. pGV831 is a streptomycin-resistant pBR325 derivative that contains a kanamycin resistance marker gene for plant cells and a site for cloning foreign genes between the 25-bp border sequences of the octopine T-region. Conjugative transfer of pGV831 derivatives to Agrobacterium and cointegration by homologous recombination between the pBR322 sequences present on pGV831 and pGV2260, can be obtained in a single step. Strains carrying the resulting cointegrated plasmids transfer and integrate T-DNA into the genome of tobacco protoplasts, and transformed tobacco calli are readily selected as resistant to kanamycin. Intact plants containing the entire DNA region between the T-DNA borders have been regenerated from such clones. In view of these properties we present pGV831 and its derivatives as vectors for efficient integration of foreign genes into plants.
Quantitative hybridization-arrest of mRNA in Xenopus oocytes using single-stranded complementary DNA or oligonucleotide probes

The expression of heterologous mRNA in Xenopus oocytes was quantitatively inhibited by coinjection of single-stranded complementary DNA or synthetic complementary oligonucleotides. The lymphokines Interleukin-2 (IL-2) and Interleukin-3 (IL-3) were used as model systems to test the effectiveness of this procedure. Messenger RNA samples were hybridized to single stranded complementary DNA or oligonucleotides, injected into oocytes and the oocyte incubation medium assayed for the presence or absence of specific translation products 48 hours later. When IL-2 mRNA was hybridized to a large excess of long (490 bases) single stranded complementary DNA, the expression of IL-2 was effectively blocked (greater than 98%). Complementary oligonucleotides (18-23 bases) were almost as effective as the polynucleotide in inhibiting IL-2 activity (greater than 95%). Oligonucleotides derived from the 5' end, middle or 3' end of the coding sequence were all effective in arresting IL-2 mRNA translation. Oligonucleotide hybrid-arrest was effective even when no NaCl was present in the hybridization buffer, indicating that the annealing reaction could occur within the oocyte after injection. Definite proof that hybrid-arrest could occur in vivo was shown by the fact that oligonucleotides injected before or after mRNA injection, while not as effective as co-injection, still showed substantial inhibition of specific mRNA translation. The oligonucleotide hybrid-arrest method was equally effective in the case of IL-3, demonstrating its general applicability.
BIONET: national computer resource for molecular biology

This paper describes briefly the BIONET National Computer Resource for Molecular Biology. This presentation is intended as information for scientists in molecular biology and related disciplines who require access to computational methods for sequence analysis. We describe the goals, and the service and research opportunities offered to the community by BIONET, the relationship of BIONET to other national and regional resources, our recent efforts toward distribution of the resource to BIONET Satellites, and procedures for investigators to gain access to the Resource.
Proposal for Improved Translation and Meaning of "Public Health" in the Republic of Macedonia

Proposal for Improved Translation and Meaning of "Public Health" in the Republic of Macedonia The translation and use of the term "public health" in the Republic of Macedonia creates confusions among students, professionals and the public. Its use and meaning in Macedonian language is associated more to the ownership over the healthcare system by the state, rather than to explain the primary goal and mission of public health to protect, promote and restore the health of the public. There is a need to clarify, change and standardize the use of this terminology in the Republic of Macedonia. Medical Faculty in Skopje should take leadership by introducing this change in the public health curriculum of the postgraduate studies.
Melanoma Immunomodulation: A War of Attrition

most common cancer, with a lifetime risk of 2.04% for men and 1.38% for women (Jemal et al., 2008; Jilaveanu et al., 2009). According to the American Cancer Society, in 2009 the number of new cases of melanoma rose to 68,720 with 8,650 new deaths attributed to the disease (ACS, 2010). There are many known factors that contribute to the formation of melanoma. One major factor influencing the increase in melanoma cases is increased exposure to ultra-violet radiation (UVR). Other risk factors include skin type, hair/eye color, the presence of dysplastic nevi and/or increased nevi, and a family history of melanoma (Jilaveanu et al., 2009). Also, mutations in BRAF, CDKN2A, and CDK4 genes have all been attributed to melanoma development. BRAF mutations have been found in 70% of all melanomas and greater than 90% of these mutations carry a single missense (single nucleotide change) mutation (Meyle & Guldberg, 2009). CDKN2A is involved in melanoma pathogenesis and is a germline mutation found in younger patients (Liu et al., 2007). CDK4 is involved in cell-cycle arrest and has been identified in 10% of melanomas (Bennett, 2008). These mutations are mostly detected in non-chronic sun-induced damage melanomas, while chronic sun-induced damage melanomas are more commonly observed. When melanoma arises, early diagnosis is crucial to survival. With early diagnosis, more than 80% of cases can be treated successfully through surgery (Zhu et al., 2009). This surgery includes excision of the tumor and surrounding tissue; lymph nodes near the tumor may also be removed if evidence of metastasis is present. Other treatments for melanoma include radiation and chemotherapy, used particularly in cases of highly aggressive and metastatic disease (ACS, 2010). Side-effects from these treatments include fatigue, malaise, and an increased susceptibility to non-melanoma cancers (Kamposioras et al., 2010). Also, these therapies are severely toxic to the patients, suggesting a need for improved, less toxic treatment options that specifically target melanoma tumors, like immunotherapy. The multiple ways that melanoma alters the immune system locally, at the site of the tumor, and systemically makes the disease difficult to treat but ideal for the study of immunomodulation (Berinstein, 2009). Immunomodulation, the alteration of the immune system or its function, is exploited in multiple forms by melanoma tumors from changes in the cellular and sub-cellular makeup of the tumor to changes in the tumor microenvironment that suppress localized and systemic attempts at disease reduction.
Automatic reading of DNA sequencing gel autoradiographs using a large format digital scanner

We have developed a large format digital scanner for several applications in nucleic acid analysis. Here we describe the scanning of autoradiographs of DNA sequencing gels and a set of programs for reading the base sequence. The programs correct distortions in the gel, recognize bands by their characteristic shape and assign bases to bands by weighting band position and intensity. The sequence read in this way is as accurate as that read by an expert.
On the tenth value distance of the photon field along the maze of high‐energy linear accelerator vaults

Abstract There is a wide range in the reported photon tenth value distance (TVD) in the maze of high‐energy linear accelerator vaults. In order to gain insight into the appropriate use of the TVD value during door design, we performed measurements of the photon dose in the maze of four vaults. In addition, our study represents the first to describe a scenario where an inner borated polyethylene (BPE) door for neutron shielding is installed in the maze downstream to Point A, the point on the maze centerline that is just visible from the isocenter. The measurements were made along the maze centerline at 1 m above the floor. In all cases, the accelerator operated at a nominal energy of 15 MV. Of the four vaults, three were equipped with an inner BPE door at a distance of 1.0–2.1 m downstream to Point A. The door was made of 10.16 cm (4″) BPE sandwiched between two 0.635 cm (1/4″) steel face plates. The photon dose in the maze without a BPE door decreases exponentially with a characteristic TVD of 6 m beyond a distance of 2.5 m from Point A. The presence of a BPE door in an identical vault not only reduces the photon intensity in the maze by about an order of magnitude, but also softens the energy spectrum with a shortened TVD of 4.7 m, significantly lessening the shielding burden at the outer maze entrance. In contrast to the common use of Point A as the reference point to specify distance, the photon dose in the maze with a BPE door located downstream to Point A can be satisfactorily described as exponential functions of the distance measured from the door, which shows good consistency among the three vaults of different room parameters.
The sequence of the Saccharomyces cerevisiae gene PHO2 codes for a regulatory protein with unusual aminoacid composition

A new centromere vector for the construction of a Saccharomyces cerevisiae gene library, allowing direct selection for DNA insert, will be described. From that library the gene for the regulatory protein PHO2 involved in PHO5 induction has been cloned by complementation of a pho2 mutation. The complementing activity was shown to be located on a 3.6 kb HindIII fragment. This fragment was used to evict the genomic copy and with appropriate genetic crosses we proved, that the cloned gene is PHO2. The DNA sequence of PHO2 was determined. Analysis of the sequence data uncovered striking homology regions with PHO4, another protein necessary for the induction of PHO5. The relevance of the observed homology will be discussed.
Skin neoplasia in small animals 2. Common feline tumours

SKIN cancer is very common in cats, the skin being the second most reported site of malignancy after lymphoid tissue. Unlike dogs, skin tumours in the cat are more likely to be malignant than benign; most benign tumours seen in dogs, such as lipomas, pilomatricomas and papillomas, are rare in cats. Cutaneous malignant melanoma and apocrine gland adenocarcinoma are similarly rare. The most common feline tumours reported in several studies in the UK and USA are fibrosarcomas, squamous cell carcinomas, and basal cell and mast cell tumours, the diagnosis and management of which are discussed in this article. It should be noted that many proliferative or ulcerative skin conditions can mimic neoplasia in the cat, such as eosinophilic granuloma complex, flea allergic dermatitis, mycoses, poxvirus, dermatophytoses and autoimmune disease.
The Health Belief Model and Preventive Health Behavior

The Health Belief Model was originally formulated to explain (preventive) health behavior. As defined by Kasl and Cobb,’ health behavior is “any activity undertaken by a person who believes himself to be healthy for the purpose of preventing disease or detecting disease in a n asymptomatic stage. ” This is in contrast with illness behavior, defined as “any activity undertaken by a person who feels ill, for the purpose of defining the state of his health and of discovering suitable remedy,” and sick-role behavior, “the activity undertaken by those who consider themselves ill for the purpose of getting well. ” The present paper is confined to the first of these areas health behavior. I t should first be noted that the three modes of behavior are not discontinuous. Hardly anyone can be found who, upon intensive questioning, would report himself free of all symptoms. Similarly, the edges between illness behavior and sick-role behavior are blurred. Nevertheless, the distinctions are valuable because they refer to modal mental states which help to account for behavior.
Physiological and Pharmacological Regulation of the STAT3 Pathway in Cancer

STAT3 is a critical oncogenic transcription factor, but how it becomes aberrantly activated in cancer is unclear. We have discovered a new pathway whose loss is associated with persistent STAT3 activation in human cancer. We found that the tumor suppressor miR-146b is a direct STAT3 target gene in normal breast epithelial cells. However, STAT regulation of miR146b is subverted in tumor cells and is suppressed by promoter methylation, which is increased in primary breast cancers. Moreover, we show that miR-146b inhibits NF-κB-dependent IL-6 production, IL-6-dependent STAT3 activation, and IL-6/STAT3-driven functional phenotypes, thereby establishing a negative feedback loop. In addition, miR-146b expression appears to be deregulated in tumors with the highest levels of activated STAT3, and is positively correlated with patient survival. Our results indicate a new mechanism of crosstalk between STAT3 and NF-κB relevant to constitutive STAT3 activation in malignancy and the role of inflammation in oncogenesis. Despite the importance of STAT3 in cancer, clinically available therapies to inhibit STAT3 are limited. A chemical genomics approach can discover drugs with novel mechanisms of action. In this manner, the FDA-approved drug atovaquone was identified to oppose the gene expression signature of STAT3. At concentrations readily achieved in human plasma, atovaquone inhibits STAT3 phosphorylation, transcriptional activity, and STAT3-dependent iv cancer cell viability. Atovaquone is not a kinase inhibitor, but instead downregulates cell-surface gp130 expression, which is required for STAT3 activation in multiple contexts. Additionally, atovaquone activates certain components of the unfolded protein response and inhibits mTOR by inducing REDD1. Importantly, higher atovaquone exposure is associated with improved diseasefree survival in patients who underwent hematopoietic stem cell transplant for hematological malignancies. These results establish atovaquone as a novel STAT3 inhibitor with evidence of anti-cancer efficacy in patients.
Diagnostic criteria for fibromyalgia: Comment on the article by Wolfe et al

approach, glenohumeral joint, 1 RCT (8); posterior approach, glenohumeral joint, 1 RCT (9); glenohumeral joint, 2 RCTs (10,11); glenohumeral joint or subacromial bursa or bicipital tendon, 9 RCTs (12–14); and supraspinatus tendon, 1 RCT (15). Many different approaches were used in these RCTs; if we segregated the patients into subgroups on the basis of these approaches, then the number of studies and patients included in our analysis would be too small to arrive at a reliable conclusion regarding the effects of these therapies. Therefore, in this meta-analysis, we did not evaluate the efficacy of hyaluronate injections for the various injection approaches. We thank Dr. Padua and colleagues for their thoughtprovoking comments regarding these important issues in our meta-analysis.
The utility of the surgical safety checklist for wound patients

The purpose of this study was to determine the frequency of changes in patient care resulting from the use of a surgical safety checklist. Data were retrospectively obtained from 233 patients. The number and types of changes made to the patients' intra‐operative management, based on the use of the checklist, were recorded. The number of patients whose management was modified as a result of the checklist was 113 (48%) out of 233. The total number of changes made was 132, and 18 patients had more than one modification made to their care plan. Further stratification was identified: among the 132 changes made, antibiotics were held or administered in 73 (55%), changes related to anaemia involving type and screen or transfusion occurred in 27 (20%), modifications made regarding anti‐coagulation occurred in 8 (7%), beta‐blockers were held in 2 (2%), an allergy was identified in 7 (5%), modifications made to the surgical procedure were 3 (2%) and a category labelled ‘other’ encompassed 9 (7%) changes. The surgical safety checklist is a standardised form of team communication that leads to modifications of the patient care plan in a large percentage of cases. The ever‐increasing complexity of medicine means that patients are at greater risk of oversight and harm without the use of a checklist.
Alternative approach to addressing infrastructure needs in biomedical engineering programs (Case of emerging economies)

This paper discusses the ways to develop low budget and high performance laboratory exercises for the purpose of the biomedical engineering education. The proposed methodology is based on the integration of 13 different sensors/actuators, 4 interfaces and 2 software, which are widely available and inexpensive. The proposed components are described separately and then integrated into specific exercises realized as virtual instruments for physiological measurements, vital signs monitoring and biomedical signal processing. Following the proposed methodology the students can use their creativity, and acquired knowledge from other disciplines to design variants of virtual instruments in order to achieve the real-world experience. Also, the economic aspects in terms of the overall system cost and the cost of its reduced variants are outlined. The ratio between the quality and cost shows that proposed approach should be very suitable for biomedical engineering education in developing countries, Keywords: biomedical engineering, education, physiological measurements, sensors, virtual