LLukas22/scidocs huggingface dataset:
Phase I studies of fluorouracil, doxorubicin and vinorelbine without (FAN) and with (SUPERFAN) folinic acid in patients with advanced breast cancer

Purpose: The Breast Cancer Site Group of the National Cancer Institute of Canada – Clinical Trials Group (NCIC-CTG) undertook two parallel phase I studies to determine the maximum tolerated dose (MTD) and recommended phase II dose of vinorelbine in combination with doxorubicin and fluorouracil (with or without folinic acid) in metastatic breast cancer. Methods: Cohorts of five patients were to receive: (a) fluorouracil 500 mg/m2 and doxorubicin 50 mg/m2 on day 1 only and escalating doses of vinorelbine (15, 20, 25, 30 mg/m2) on days 1, 8 and 15 every 3 weeks (FAN regimen), or (b) fluorouracil 340 mg/m2 and folinic acid 200 mg/m2 on days 1, 2, 3, 4 and 5, doxorubicin 40 mg/m2 on day 1 only and escalating doses of vinorelbine (15, 20, 25, 30 mg/m2) on day 1 and again on day 5 every 4 weeks (SUPERFAN regimen). Eligibility included measurable or evaluable metastatic breast cancer and having received neither previous chemotherapy for metastatic disease nor anthracycline-containing adjuvant therapy. Results: Of 26 and 12 patients enrolled in the FAN and SUPERFAN regimens, 26 and 12 were evaluable for toxicity and 21 and 9 for response, respectively. Median ages were 60.3 years (41–71 years) and 64.2 years (51–73 years). Both regimens required amendment after the first cohort with an original day-15 vinorelbine dose omitted from the FAN regimen and more prolonged nadir granulocyte counts allowed. Myelosuppression was dose limiting. MTDs in the FAN and SUPERFAN regimens were vinorelbine 25 mg/m2 and 20 mg/m2. Other toxicities included mucositis, septicemia and febrile neutropenia. Peripheral neuropathy and constipation were mild. Of the 21 FAN patients evaluable for response, 3 (14%) had complete responses and 7 (33%) had partial responses, for an overall response rate of 48%; 9 (43%) had stable disease and 2 (9%) had progressive disease as their best response. Of the nine SUPERFAN patients evaluable for response, none had a complete response. There were two (22%) with partial responses, and six (67%) had stable disease and one (11%) had progressive disease as their best response. Conclusions: The SUPERFAN regimen was too toxic to pursue even at the lowest dose. The recommended phase II starting dose for the FAN regimen was vinorelbine 20 mg/m2. Although these were phase I studies response rates in evaluable patients were less than expected and toxicity did not allow the use of as much vinorelbine in the combinations as had been anticipated. The limited response data from our study would imply that combining vinorelbine with more toxic agents may not enhance response rates and may defeat the advantage of tolerability, especially in elderly patients.
Follow-up of high-risk HPV positive women by combined cytology and bi-marker CADM1/MAL methylation analysis on cervical scrapes.

OBJECTIVES
Triage of HPV screen-positive women is needed to identify those with underlying cervical intraepithelial neoplasia grade 2/3 or worse (CIN2/3+). Presently, cytology on a physician-taken cervical scrape is mostly accepted as triage test, but needs follow-up testing in order not to miss severe disease. Here, we evaluated the performance of combined cytology and bi-marker CADM1/MAL-methylation analysis as triage test on physician-taken cervical scrapes of HPV positive women.


METHODS
In this post-hoc analysis, we used 364 left-over HPV positive cytology triage samples of participants of a randomized controlled trial (PROHTECT-3: n=46,001) performed in population-based cervical screening. Study endpoints were CIN2+ and CIN3+ detection. Cytology testing with and without methylation marker analysis was evaluated with regard to sensitivity, specificity, positive and negative predictive value, and referral rate.


RESULTS
Bi-marker CADM1/MAL-methylation positivity increased proportionally with severity of underlying lesions. Overall, cytology and bi-marker CADM1/MAL-methylation analysis yielded similar performances with regard to CIN3+ detection, yet in combination a significantly higher sensitivity for CIN3+ (88.7%) was obtained at a specificity of 53.6% and a colposcopy referral rate of 53.6%. The combined strategy detected all six cervical cancers, whereas triage by cytology alone failed to detect two of them.


CONCLUSIONS
Cytology and bi-marker CADM1/MAL-methylation analysis perform complementary for CIN2+/CIN3+ detection when used as triage tool on cervical scrapes of HPV positive women. This approach not only results in a higher CIN3+ sensitivity than cytology triage with an acceptable referral rate, but also seems to reduce the risk of missing cervical cancers and advanced high-grade lesions.
End-to-End Concept Word Detection for Video Captioning, Retrieval, and Question Answering

We propose a high-level concept word detector that can be integrated with any video-to-language models. It takes a video as input and generates a list of concept words as useful semantic priors for language generation models. The proposed word detector has two important properties. First, it does not require any external knowledge sources for training. Second, the proposed word detector is trainable in an end-to-end manner jointly with any video-to-language models. To effectively exploit the detected words, we also develop a semantic attention mechanism that selectively focuses on the detected concept words and fuse them with the word encoding and decoding in the language model. In order to demonstrate that the proposed approach indeed improves the performance of multiple video-to-language tasks, we participate in all the four tasks of LSMDC 2016 [18]. Our approach has won three of them, including fill-in-the-blank, multiple-choice test, and movie retrieval.
ABC transporters in Arthropods : genomic comparison and role in insecticide transport and resistance

About a 100 years ago, the Drosophila white mutant marked the birth of Drosophila genetics. The white gene turned out to encode the first well studied ABC transporter in arthropods. The ABC gene family is now recognized as one of the largest transporter families in all kingdoms of life. The majority of ABC proteins function as primary-active transporters that bind and hydrolyze ATP while transporting a large diversity of substrates across lipid membranes. Although extremely well studied in vertebrates for their role in drug resistance, less is known about the role of this family in the transport of endogenous and exogenous substances in arthropods. The ABC families of five insect species, a crustacean and a chelicerate have been annotated in some detail. We conducted a thorough phylogenetic analysis of the seven arthropod and human ABC protein subfamilies, to infer orthologous relationships that might suggest conserved function. Most orthologous relationships were found in the ABCB half transporter, ABCD, ABCE and ABCF subfamilies, but specific expansions within species and lineages are frequently observed and discussed. We next surveyed the role of ABC transporters in the transport of xenobiotics/plant allelochemicals and their involvement in insecticide resistance. The involvement of ABC transporters in xenobiotic resistance in arthropods is historically not well documented, but an increasing number of studies using unbiased differential gene expression analysis now points to their importance. We give an overview of methods that can be used to link ABC transporters to resistance. ABC proteins have also recently been implicated in the mode of action and resistance to Bt toxins in Lepidoptera. Given the enormous interest in Bt toxicology in transgenic crops, such findings will provide an impetus to further reveal the role of ABC transporters in arthropods. 2014 The Authors. Published by Elsevier Ltd. Open access under CC BY-NC-ND license.
The Construct Validity of Student Engagement: A Confirmatory Factor Analysis Approach

As institutions seek to promote student engagement on campus, the National Survey of Student Engagement (NSSE) is increasingly being used to chart progress and compare results using the Five Benchmark Scores. While recent research has begun to decompose the five benchmarks in a variety of ways; few research studies have sought to explore the underlying structure of these five benchmarks, their interdependence, and the extent to which the items do reflect those five dimensions. This study begins to address the instrument’s construct validity by submitting a single, first-time freshman cohort’s NSSE responses to a confirmatory factor analysis, and proposes as an alternative, eight ‘‘dimensions’’ of student engagement that fit this set of data slightly better and in a more useful way. Results have practical implications for institutions utilizing NSSE, but also contain conceptual implications pertaining to the application of these benchmarks.
cts: An R Package for Continuous Time Autoregressive Models via Kalman Filter

We describe an R package cts for fitting a modified form of continuous time autoregressive model, which can be particularly useful with unequally sampled time series. The estimation is based on the application of the Kalman filter. The paper provides the methods and algorithms implemented in the package, including parameter estimation, spectral analysis, forecasting, model checking and Kalman smoothing. The package contains R functions which interface underlying Fortran routines. The package is applied to geophysical and medical data for illustration.
End-to-End Reinforcement Learning for Automatic Taxonomy Induction

§ Action (term-pair) Representation • Dependency Paths between x, y • Wx: Word Embedding of x • Wy: Word Embedding of y • F(x, y): Surface (Ends with, Contains, etc.), Frequency (pattern-based co-occur info), and Generality (edge not too general or narrow) Features § Performance Study on End-to-End Taxonomy Induction: • WordNet (533/144/144 taxonomies for training, validation, and test set, size (10, 50], depth=4, animals, daily necessities, etc.) § Compared methods: • TAXI [3]: pattern-based method that ranked 1st in the SemEval-2016 Task 13 competition • HypeNET [4]: state-of-the-art hypernymy detection method • HypeNET + MST (maximum spanning tree): post-processing of HypeNET to prune the hypernym graph into a tree • Bansal et al. (2014) [1]: state-of-the-art taxonomy induction method • SubSeq [2]: state-of-the-art results on the SemEval-2016 Task 13 • Taxo-RL (RE, with virtual root embedding), Taxo-RL (NR, with new root addition), Taxo-RL (NR) + FG (with frequency and generality features) • Taxo-RL (partial, allows partial taxonomy), Taxo-RL (full, has to use all terms in the vocabulary)
Diagnosis and treatment of bacteremia and endocarditis due to Staphylococcus aureus. A clinical guideline from the Spanish Society of Clinical Microbiology and Infectious Diseases (SEIMC).

Both bacteremia and infective endocarditis caused by Staphylococcus aureus are common and severe diseases. The prognosis may darken not infrequently, especially in the presence of intracardiac devices or methicillin-resistance. Indeed, the optimization of the antimicrobial therapy is a key step in the outcome of these infections. The high rates of treatment failure and the increasing interest in the influence of vancomycin susceptibility in the outcome of infections caused by both methicillin-susceptible and -resistant isolates has led to the research of novel therapeutic schemes. Specifically, the interest raised in recent years on the new antimicrobials with activity against methicillin-resistant staphylococci has been also extended to infections caused by susceptible strains, which still carry the most important burden of infection. Recent clinical and experimental research has focused in the activity of new combinations of antimicrobials, their indication and role still being debatable. Also, the impact of an appropriate empirical antimicrobial treatment has acquired relevance in recent years. Finally, it is noteworthy the impact of the implementation of a systematic bundle of measures for improving the outcome. The aim of this clinical guideline is to provide an ensemble of recommendations in order to improve the treatment and prognosis of bacteremia and infective endocarditis caused by S. aureus, in accordance to the latest evidence published.
Surface crystallization of liquid normal-alkanes.

X-ray scattering and surface tension measurements reveal the formation of a crystalline monolayer on the surface of liquid n-alkanes at about 3 C above the bulk solidification temperature. The molecules in the monolayer are hexagonally packed and oriented normal to the surface. The single solid monolayer persists down to the bulk solidification temperature, thus exhibiting a very limited partial wetting.
Dexamethasone added to Local Lidocaine for Infiltration along the Spinal-Epidural Needle Pathway Decreases Incidence and Severity of Backache after Gynecological Surgery

BACKGROUND
The aim of this study was to evaluate the effect of dexamethasone added to local lidocaine infiltration on incidence and severity of backache after combined spinal-epidural anesthesia for gynecological surgery.


MATERIAL AND METHODS
We randomly allocated 160 patients to receive either local lidocaine infiltration along the pathway of the spinal-epidural needle (Group L) or local dexamethasone and lidocaine infiltration (Group DL). The incidence and scores for back pain were evaluated on the first, second, and third day (acute lumbago) and first, second, and sixth month (chronic lumbago) after surgery. Fentanyl consumption for management of back pain was recorded.


RESULTS
The incidence of acute, subacute, and chronic back pain was significantly lower in the DL group than the L group (P<0.05 for all comparisons). The VAS score for back pain on the first and second day and first and second month, were significantly lower in the DL group than the L group (P=0.0028, P=0.017; P<0.001, both), but there were no significant differences on the third day and sixth month. Fentanyl consumption in the first 3 postoperative days was significantly lower in the DL group than in the L group (P<0.001). The incidence of back pain during the first, second, and sixth month in patients who did not have preoperative lumbago were significantly lower in the DL group than in the L group (P<0.001, both).


CONCLUSIONS
Addition of dexamethasone to local lidocaine infiltration effectively decreases the incidence and severity of back pain after combined spinal-epidural anesthesia implemented for gynecological surgery.
Onychomycosis and diabetes.

OBJECTIVE
This study aims to discuss factors specific to diabetics in the diagnosis and treatment of onychomycosis.


DISCUSSION
Onychomycosis has the potential to cause severe complications in diabetics and should be treated promptly. The existence of comorbid conditions and potential for drug-drug interactions complicates the selection of an appropriate treatment regimen. The role of Candida in onychomycosis is controversial but may be of increased significance in the diabetic population due to an underlying vulnerability to this organism.


CONCLUSIONS
Terbinafine is an excellent choice in diabetics due to its low risk of drug-drug interaction and proven efficacy against the typical pathogens that cause onychomycosis. Itraconazole, while an effective treatment for onychomycosis, is not a first-choice therapy due to its black-box cardiac warning and numerous drug interactions. Larger studies are needed in diabetics to determine the frequency of candidal nail infections.
On the Interrelations and Economic Implications of Economic , Social , Political , and Normative Factors : Reflections From Two Late Medieval Societies

This paper utilizes transaction cost economics, game theory, and insights from sociology and psychology to conduct a comparative historical study of the institutional structure of two late Medieval societies, one from the Muslim world and one from the Latin world. The analysis indicates that understanding institutional path dependence, distinct trajectories of organizational development, and the relations between institutions and economic efficiency requires analyzing institutional structure as a system of inter-related economic, social, political, and normative components. Interestingly, the distinct institutional structures found in the late medieval period resemble those found by social psychologists to differentiate contemporary developing and developed economies. Hence this paper suggests the historical importance of distinct cultures and the related societal organizations in economic development. * This paper was prepared under a cooperative agreement between the Institute for Policy Reform (IPR) and the Agency for International Development (AID), Cooperative Agreement No. PDC-0095-A-001126-00. Views expressed in this paper are those of the author and not necessarily those of IPR or AID. The paper draws from my earlier works, particularly, "Cultural Beliefs and the Organization of Society," the Journal of Political Economy October, 1994. The research reflected in these papers was supported by National Science Foundation Grants # 9009598 and 9223974. Donald N. McCloskey, Bent Holmstrom, and anonymous referee provided helpful comments.
Crowdsourcing, Attention and Productivity

The tragedy of the digital commons does not prevent the copious voluntary production of content that one witnesses in the web. We show through an analysis of a massive data set from YouTube that the productivity exhibited in crowdsourcing exhibits a strong positive dependence on attention, measured by the number of downloads. Conversely, a lack of attention leads to a decrease in the number of videos uploaded and the consequent drop in productivity, which in many cases asymptotes to no uploads whatsoever. Moreover, uploaders compare themselves to others when having low productivity and to themselves when exceeding a threshold. 1 ar X iv :0 80 9. 30 30 v1 [ cs .C Y ] 1 7 Se p 20 08 We are witnessing an inversion of the traditional way by which content has been generated and consumed over the centuries. From photography to news and encyclopedic knowledge, the centuries-old pattern has been one in which a relatively few people and organizations produce content and most people consume it. With the advent of the web and the ease with which one can migrate content to it, that pattern has reversed, leading to a situation whereby millions create content in the form of blogs, news, videos, music, etc. and relatively few can attend to it all. This phenomenon, which goes under the name of crowdsourcing, is exemplified by websites such as Digg, Flicker, YouTube, and Wikipedia, where content creation without the traditional quality filters manages to produce sought out movies, news and even knowledge that rivals the best encyclopedias. That such content is valued is confirmed by the fact that access to these sites accounts for a sizable percentage of internet traffic. For example, as of June, 2007 YouTube alone comprised approximately 20% of all HTTP traffic, or nearly 10% of all traffic on the Internet [2]. What makes crowdsourcing both interesting and puzzling is the underlying dilemma facing every contributor, which is best exemplified by the well-known tragedy of the commons. In such dilemmas, a group of people attempts to provide a common good in the absence of a central authority. In the case of crowdsourcing, the common good is in the form or videos, music, or encyclopedic knowledge that can be freely accessed by anyone. Furthermore, the good has jointness of supply, which means that its consumption by others does not affect the amounts that other users can use. And since it is nearly impossible to exclude non contributors from using the common good, it is rational for individuals not to upload content and free ride on the production of others. The dilemma ensues when every individual can reason this way and free ride on the efforts of others, making everyone worse off—thus the tragedy of the digital commons [1, 3, 7, 5, 10]. And yet paradoxically, there is ample evidence that while the ratio of contributions to downloads is indeed small, the growth in content provision persists at levels that are hard to understand if analyzed from a public goods point of view. One possible explanation for this puzzling behavior, which we explore in this paper, is that those contributing to the digital commons
Estimating Location Using Wi-Fi

This department presents the results of the first Data Mining Contest held at the 2007 International Conference on Data Mining.
High-dose treosulfan in patients with relapsed or refractory high-grade lymphoma receiving tandem autologous blood stem cell transplantation

Summary:This phase I/II study evaluated high-dose treosulfan in patients with high-grade lymphoma. In all, 21 patients (median age 51, 25–60 years) with primary refractory disease (n=3) or early (n=11) or late (n=7) relapse received DexaBEAM and one course etoposide for cytoreduction and PBPC mobilization. Subsequently, 16 patients received 30 g/m2 treosulfan and 140 mg/m2 melphalan, followed by autologous transplantation. Nine patients received a 2nd high-dose treatment (HDT) with 30 g/m2 treosulfan and 750 mg/m2 thiotepa. Recovery time to >1/nl leukocytes and >25/nl thrombocytes was 8.9 (range 8–11) and 11.9 (8–16) days after 1st and 9.6 (7–13) and 13 (9–19) days after 2nd HDT. Reversible grade 3 or 4 nonhematologic toxicities included mucositis (n=7), infection (n=7) and one episode of re-entry tachycardia. Two treatment-related deaths occurred after 2nd HDT. Since three dose-limiting toxicities occurred among nine patients receiving tandem HDT, 30 g/m2 of treosulfan was considered MTD in this setting. Patients with late compared to early relapse or refractory disease had a higher probability of CR (6/7 vs 3/14 patients, P=0.017) and overall survival (71 vs 21%, P<0.05, 24–49 months follow-up). In conclusion, high-dose treosulfan as major therapy component induces sustained complete remissions in relapsed high-grade lymphoma with acceptable toxicity.
A Fresh Approach to a Model for Quality in Higher Education

There is a considerable urgency for the development of an appropriate model for quality in Higher Education. Attempts to apply the Quality Management models from industry have not been fully successful. In applying any model it is necessary to see the service and education aspects separately. Quality Management models are quite appropriate to the former. For the latter a number of models of excellence for a university proposed in the recent literature, centred around student learning, are reviewed. It is argued that a composite holistic model for quality in Higher Education can be developed addressing the service and education aspects synergistically.