Topic selection in industry experiments

This paper shares our experience with initial negotiation and topic elicitation process for conducting industry experiments in six software development organizations in Finland. The process involved interaction with company representatives in the form of both multiple group discussions and separate face-to-face meetings. Fitness criteria developed by researchers were applied to the list of generated topics to decide on a common topic. The challenges we faced include diversity of proposed topics, communication gaps, skepticism about research methods, initial disconnect between research and industry needs, and lack of prior work relationship. Lessons learned include having enough time to establish trust with partners, importance of leveraging the benefits of training and skill development that are inherent in the experimental approach, uniquely positioning the experimental approach within the landscape of other validation approaches more familiar to industrial partners, and introducing the fitness criteria early in the process.

The Role of Passage Topic Knowledge in Typical and Poor Comprehenders' Recall

This dissertation examines the role of topic knowledge (TK) in comprehension among typical readers and those with Specifically Poor Comprehension (SPC), i.e., those who demonstrate deficits in understanding what they read despite adequate decoding. Previous studies of poor comprehension have focused on weaknesses in specific skills, such as word decoding and inferencing ability, but this dissertation examined a different factor: whether deficits in availability and use of TK underlie poor comprehension. It is well known that TK tends to facilitate comprehension among typical readers, but its interaction with working memory and word decoding is unclear, particularly among participants with deficits in these skills. Across several passages, we found that SPCs do in fact have less TK to assist their interpretation of a text. However, we found no evidence that deficits in working memory or word decoding ability make it difficult for children to benefit from their TK when they have it. Instead, children across the skill spectrum are able to draw upon TK to assist their interpretation of a passage. Because TK is difficult to assess and studies vary in methodology, another goal of this dissertation was to compare two methods for measuring it. Both approaches score responses to a concept question to assess TK, but in the first, a human rater assigns a score whereas in the second, a computer algorithm, Latent Semantic Analysis (LSA; Landauer & Dumais, 1997) assigns a score. We found similar results across both methods of assessing TK, suggesting that a continuous measure is not appreciably more sensitive to variations in knowledge than discrete human ratings. This study contributes to our understanding of how best to measure TK, the factors that moderate its relationship with recall, and its role in poor comprehension. The findings suggest that teaching practices that focus on expanding TK are likely to improve comprehension across readers with a variety of abilities.

Which Anesthesia Regimen Is Best to Reduce Morbidity and Mortality in Lung Surgery? A Multicenter Randomized Controlled Trial.

BACKGROUND One-lung ventilation during thoracic surgery is associated with hypoxia-reoxygenation injury in the deflated and subsequently reventilated lung. Numerous studies have reported volatile anesthesia-induced attenuation of inflammatory responses in such scenarios. If the effect also extends to clinical outcome is yet undetermined. We hypothesized that volatile anesthesia is superior to intravenous anesthesia regarding postoperative complications. METHODS Five centers in Switzerland participated in the randomized controlled trial. Patients scheduled for lung surgery with one-lung ventilation were randomly assigned to one of two parallel arms to receive either propofol or desflurane as general anesthetic. Patients and surgeons were blinded to group allocation. Time to occurrence of the first major complication according to the Clavien-Dindo score was defined as primary (during hospitalization) or secondary (6-month follow-up) endpoint. Cox regression models were used with adjustment for prestratification variables and age. RESULTS Of 767 screened patients, 460 were randomized and analyzed (n = 230 for each arm). Demographics, disease and intraoperative characteristics were comparable in both groups. Incidence of major complications during hospitalization was 16.5% in the propofol and 13.0% in the desflurane groups (hazard ratio for desflurane vs. propofol, 0.75; 95% CI, 0.46 to 1.22; P = 0.24). Incidence of major complications within 6 months from surgery was 40.4% in the propofol and 39.6% in the desflurane groups (hazard ratio for desflurane vs. propofol, 0.95; 95% CI, 0.71 to 1.28; P = 0.71). CONCLUSIONS This is the first multicenter randomized controlled trial addressing the effect of volatile versus intravenous anesthetics on major complications after lung surgery. No difference between the two anesthesia regimens was evident.

Nitric oxide synthase inhibition in sepsis? Lessons learned from large-animal studies

Nitric Oxide (NO) plays a controversial role in the pathophysiology of sepsis and septic shock. Its vasodilatory effects are well known, but it also has pro- and antiinflammatory properties, assumes crucial importance in antimicrobial host defense, may act as an oxidant as well as an antioxidant, and is said to be a vital poison for the immune and inflammatory network. Large amounts of NO and peroxynitrite are responsible for hypotension, vasoplegia, cellular suffocation, apoptosis, lactic acidosis, and ultimately multiorgan failure. Therefore, NO synthase (NOS) inhibitors were developed to reverse the deleterious effects of NO. Studies using these compounds have not met with uniform success however, and a trial using the nonselective NOS inhibitor N-G-methyl-L-arginine hydrochloride was terminated prematurely because of increased mortality in the treatment arm despite improved shock resolution. Thus, the issue of NOS inhibition in sepsis remains a matter of debate. Several publications have emphasized the differences concerning clinical applicability of data obtained from unresuscitated, hypodynamic rodent models using a pretreatment approach versus resuscitated, hyperdynamic models in high-order species using posttreatment approaches. Therefore, the present review focuses on clinically relevant large-animal studies of endotoxin or living bacteria-induced, hyperdynamic models of sepsis that integrate standard day-today care resuscitative measures.

Inter- and intralaboratory variation of in vitro diffusion cell measurements: An international multicenter study using quasi-standardized methods and materials

In vitro measurements of skin absorption are an increasingly important aspect of regulatory studies, product support claims, and formulation screening. However, such measurements are significantly affected by skin variability. The purpose of this study was to determine inter- and intralaboratory variation in diffusion cell measurements caused by factors other than skin. This was attained through the use of an artificial (silicone rubber) rate-limiting membrane and the provision of materials including a standard penetrant, methyl paraben (MP), and a minimally prescriptive protocol to each of the 18 participating laboratories. Standardized calculations of MP flux were determined from the data submitted by each laboratory by applying a predefined mathematical model. This was deemed necessary to eliminate any interlaboratory variation caused by different methods of flux calculations. Average fluxes of MP calculated and reported by each laboratory (60 +/- 27 mug cm(-2) h(-1), n = 25, range 27-101) were in agreement with the standardized calculations of MP flux (60 +/- 21 mug cm(-2) h(-1), range 19-120). The coefficient of variation between laboratories was approximately 35% and was manifest as a fourfold difference between the lowest and highest average flux values and a sixfold difference between the lowest and highest individual flux values. Intra-laboratory variation was lower, averaging 10% for five individuals using the same equipment within a single laboratory. Further studies should be performed to clarify the exact components responsible for nonskin-related variability in diffusion cell measurements. It is clear that further developments of in vitro methodologies for measuring skin absorption are required. (C) 2005 Wiley-Liss, Inc.

Organization studies as an applied science:the generation and use of academic knowledge about organizations : introduction to the special issue

The relationship between theory and practice has been discussed in the social sciences for generations. Academics from management and organization studies regularly lament the divide between theory and practice. They regret the insufficient academic knowledge of managerial problems and their solutions, and criticize the scholarly production of theories that are not relevant for organizational practice (Hambrick 1994). Despite the prevalence of this topic in academic discourse, we do not know much about what kind of academic knowledge would be useful to practice, how it would be produced and how the transfer of knowledge between theory and practice actually works. In short, we do not know how we can make academic work more relevant for practice or even whether this would be desirable. In this introduction to the Special Issue, we apply philosophical, theoretical and empirical perspectives to examine the challenges of studying the generation and use of academic knowledge. We then briefly describe the contribution of the seven papers that were selected for this Special Issue. Finally, we discuss issues that still need to be addressed, and make some proposals for future avenues of research.

Originator or propagator? Incorporating social role theory into topic models for twitter content analysis

A large number of studies have been devoted to modeling the contents and interactions between users on Twitter. In this paper, we propose a method inspired from Social Role Theory (SRT), which assumes that a user behaves differently in different roles in the generation process of Twitter content. We consider the two most distinctive social roles on Twitter: originator and propagator, who respectively posts original messages and retweets or forwards the messages from others. In addition, we also consider role-specific social interactions, especially implicit interactions between users who share some common interests. All the above elements are integrated into a novel regularized topic model. We evaluate the proposed method on real Twitter data. The results show that our method is more effective than the existing ones which do not distinguish social roles. Copyright 2013 ACM.

Studies in Aetiology and Historical Methodology in Herodotus

This dissertation interrogates existing scholarly paradigms regarding aetiology in the Histories of Herodotus in order to open up new avenues to approach a complex and varied topic. Since aetiology has mostly been treated as the study of cause and effect in the Histories, this work expands the purview of aetiology to include Herodotus’ explanations of origins more generally. The overarching goal in examining the methodological principles of Herodotean aetiology is to show the extent to which they resonate across the Histories according to their initial development in the proem, especially in those places that seem to deviate from the work’s driving force (i.e. the Persian Wars). Though the focus is on correlating the principles espoused in the proem with their deployment in Herodotus’ ethnographies and other seemingly divergent portions of his work, the dissertation also demonstrates the influence of these principles on some of the more “historical” aspects of the Histories where the struggle between Greeks and barbarians is concerned. The upshot is to make a novel case not only for the programmatic significance of the proem, but also for the cohesion of Herodotean methodology from cover to cover, a perennial concern for scholars of Greek history and historiography.

Chapter One illustrates how the proem to the Histories (1.1.0-1.5.3) prefigures Herodotus’ engagement with aetiological discussions throughout the Histories. Chapter Two indicates how the reading of the proem laid out in Chapter One allows for Herodotus’ deployment of aetiology in the Egyptian logos (especially where the pharaoh Psammetichus’ investigation of the origins of Egyptian language, nature, and custom are concerned) to be viewed within the methodological continuum of the Histories at large. Chapter Three connects Herodotus’ programmatic interest in the origins of erga (i.e. “works” or “achievements” manifested as monuments and deeds of abstract and concrete sorts) with the patterns addressed in Chapters One and Two. Chapter Four examines aetiological narratives in the Scythian logos and argues through them that this logos is as integral to the Histories as the analogous Egyptian logos studied in Chapter Two. Chapter Five demonstrates how the aetiologies associated with the Greeks’ collaboration with the Persians (i.e. medism) in the lead-up to the battle of Thermopylae recapitulate programmatic patterns isolated in previous chapters and thereby extend the methodological continuum of the Histories beyond the “ethnographic” logoi to some of the most representative “historical” logoi of Herodotus’ work. Chapter Six concludes the dissertation and makes one final case for methodological cohesion by showing the inextricability of the end of the Histories from its beginning.

Multicenter randomized phase II clinical trial comparing neoadjuvant oxaliplatin, capecitabine, and preoperative radiotherapy with or without cetuximab followed by total mesorectal excision in patients with high-risk rectal cancer (EXPERT-C).

PURPOSE: To evaluate the addition of cetuximab to neoadjuvant chemotherapy before chemoradiotherapy in high-risk rectal cancer. PATIENTS AND METHODS: Patients with operable magnetic resonance imaging-defined high-risk rectal cancer received four cycles of capecitabine/oxaliplatin (CAPOX) followed by capecitabine chemoradiotherapy, surgery, and adjuvant CAPOX (four cycles) or the same regimen plus weekly cetuximab (CAPOX+C). The primary end point was complete response (CR; pathologic CR or, in patients not undergoing surgery, radiologic CR) in patients with KRAS/BRAF wild-type tumors. Secondary end points were radiologic response (RR), progression-free survival (PFS), overall survival (OS), and safety in the wild-type and overall populations and a molecular biomarker analysis. RESULTS: One hundred sixty-five eligible patients were randomly assigned. Ninety (60%) of 149 assessable tumors were KRAS or BRAF wild type (CAPOX, n = 44; CAPOX+C, n = 46), and in these patients, the addition of cetuximab did not improve the primary end point of CR (9% v 11%, respectively; P = 1.0; odds ratio, 1.22) or PFS (hazard ratio [HR], 0.65; P = .363). Cetuximab significantly improved RR (CAPOX v CAPOX+C: after chemotherapy, 51% v 71%, respectively; P = .038; after chemoradiation, 75% v 93%, respectively; P = .028) and OS (HR, 0.27; P = .034). Skin toxicity and diarrhea were more frequent in the CAPOX+C arm. CONCLUSION: Cetuximab led to a significant increase in RR and OS in patients with KRAS/BRAF wild-type rectal cancer, but the primary end point of improved CR was not met.

STARD 2015: an updated list of essential items for reporting diagnostic accuracy studies

Incomplete reporting has been identified as a major source of avoidable waste in biomedical research.
Essential information is often not provided in study reports, impeding the identification, critical
appraisal, and replication of studies. To improve the quality of reporting of diagnostic accuracy
studies, the Standards for Reporting Diagnostic Accuracy (STARD) statement was developed. Here
we present STARD 2015, an updated list of 30 essential items that should be included in every
report of a diagnostic accuracy study. This update incorporates recent evidence about sources of
bias and variability in diagnostic accuracy and is intended to facilitate the use of STARD. As such,
STARD 2015 may help to improve completeness and transparency in reporting of diagnostic accuracy
studies.

Safety and Efficacy of Oral Fexofenadine in Children with Seasonal Allergic Rhinitis - a Pooled Analysis of Three Studies

Allergic rhinitis is one of the most common clinical conditions in children; however, data regarding the safety of antihistamines in children with seasonal allergic rhinitis are limiting. To evaluate the safety and efficacy of fexofenadine in children with seasonal allergic rhinitis, data were pooled from three, double-blind, randomized, placebo-controlled, parallel-group, 2-week trials in children (6-11 year) with seasonal allergic rhinitis. All studies assessed fexofenadine HCl 30 mg b.i.d.; two studies included fexofenadine HCl at 15 and 60 mg b.i.d. Patients (and investigators) reported any adverse events during the trial. Physical examinations, including measurements of vital signs and laboratory tests, were performed. Efficacy assessments (total symptom score and individual symptom scores) were evaluated. Exposure to fexofenadine HCl 30 mg b.i.d. and to any fexofenadine dose exceeded 10,000 and 17,000 patient days, respectively. Incidences of adverse events, and discontinuations because of adverse events, were low and similar across treatment groups. In the placebo group, 24.4% of subjects reported adverse events compared with 24.1% for fexofenadine HCl 30 mg b.i.d., and 28.4% for all fexofenadine-treated groups. The most common adverse event overall was headache (4.3% placebo; 5.8% fexofenadine HCl 30 mg b.i.d.; and 7.2% any fexofenadine doses). Treatment-related adverse events were similar across treatment groups with no sedative effects. Fexofenadine HCl 30 mg b.i.d. was significantly superior to placebo in reducing the total symptom score and all individual seasonal allergic rhinitis symptoms, including nasal congestion (p < 0.05). Fexofenadine, at doses of up to 60 mg b.i.d., is safe and non-sedating, and fexofenadine HCl 30 mg b.i.d. effectively reduces all seasonal allergic rhinitis symptoms in children aged 6-11 years.

Functional studies of lignin biosynthesis genes and putative flowering gene in Miscanthus x giganteus and studies on indolyl glucosinolate biosynthesis and translocation in Brassica oleracea

The first topic area of this thesis involved studies on the accumulation and translocation of glucosinolates (GSs), bioactive secondary plant compounds, in broccoli plants. Changes in GS accumulation and gene expression levels in response to exogeneous methyl jasmonate (MeJA) treatment were analyzed in different tissue types at different developmental stages of broccoli. Greater accumulation of GSs with MeJA treatment was observed in apical leaves of broccoli seedlings and florets of plants at harvest maturity. Increases in indolyl GS in apical leaves of seedlings and florets were coupled with the up-regulation of indolyl GS biosynthesis genes. The accumulation of indolyl GSs appears to be modulated by MeJA treatment in an organ-specific manner for optimal distribution of defense substances in the plant. Metabolic profiling of hydrophilic metabolites using GC-MS demonstrated increased accumulation of various phenolics, ascorbates and amino acids in broccoli tissues after MeJA treatment. Distinct changes in carbohydrate levels observed between different tissues (vegetative leaves and floret tissues) of broccoli plants after treatment suggest that carbon metabolism is differentially modulated by MeJA treatment in different tissue types depending on sink-source relationships. Reduced levels of hexose sugars and tricarboxylic acid intermediates after MeJA treatment may reflect the increased requirement for carbon and energy needed to drive secondary product biosynthesis to accumulate metabolites for defense against insects and other herbivores. Substantial increases of indolyl and aromatic GSs after exogenous treatment with MeJA in stem and petioles of seedlings and the existence of intact indolyl-GS forms in phloem exudates suggest enhanced de novo synthesis in combination with active transport. Indoly GSs share structural similarities with the auxin, IAA, and may interact with components of the auxin transport system for intra- and extra-cellular transport or translocation. Application of the auxin efflux inhibitor, 1-naphthylphthalamic acid (NPA) reduced MeJA-mediated accumulation of indolyl GSs in broccoli florets and seedling tissues. NPA did not inhibit expression of indolyl GS biosynthesis genes shown to be upregulated by MeJA treatment or the accumulation of tryptophan, the amino acid precursor of indolyl GSs. Exogenous application of benzyl GS to Arabidopsis roots induced ectopic expression of the PIN1 protein associated with the auxin transport system similar to treatment with NPA, again suggesting GS interaction with the auxin efflux carrier system. The inhibitory effect of NPA on MeJA-mediated accumulation of GS may be due to competitive binding of NPA to auxin efflux carrier components and that GS transport is mediated by the auxin transport system. The inhibitory effect of NPA on indolyl and aromatic GS accumulation and the bioactivity of exogenous treatment of these GS compounds in PIN1 localization, Arabidopsis root growth, and gravitrophic response suggest that indolyl and aromatic GSs may be antagonistic to IAA transport and biosynthesis. Indolyl and aromatic GSs can also be potentially converted into IAA by hydrolysis. This intrinsic feature of GSs may be the part of a sophisticated regulatory process where the metabolic pathways in the plant shift from active growth to a reversible defense posture in response to biotic or abiotic stress. It seems likely that indolyl and aromatic GSs are important compounds that provide connections between jasmonate and auxin signaling. Further studies are required to reveal the regulatory mechanism for crosstalk between the two hormones. The third part of this research was to investigate effect of selenium fertilization and MeJA treatment on accumulation of GSs in broccoli florets. Increasing dietary intake of the element selenium (Se) has been shown to reduce the risk of cancer. Simultaneous enhancement of both Se and GS concentrations in broccoli floret tissue were conducted through the combined treatment of MeJA with Se fertilization. A low level of Se fertilization (concentration) with MeJA treatment displayed no significant changes in total aliphatic GS concentrations with 90% and 50% increases in indolyl and total GSs concentrations, respectively. This result suggests that Se- and GS-enriched broccoli with improved health-promoting properties can be generated by this combined treatment. The second topic of this thesis was conducted to provide basic information required to improve biomass quality and productivity and develop tools for gene transformation in Miscanthus x giganteus. The perennial rhizomatous grass, Miscanthus x giganteus is an ideal biomass crop due to its rapid vegetative growth and high biomass yield potential. As a naturally occurring sterile hybrid, M. x giganteus must be propagated vegetatively by mechanicalling divided rhizomes or from micropropagated plantlets. The effect of callus type, age and culture methods on regeneration competence was studied to improve regeneration efficiency and shorten the period of tissue culture in M. x giganteus propagation. Seven lignin biosynthesis genes and one putative flowering gene were isolated from M. x giganteus by PCR reactions using maize othologous sequences. Southern hybridization and nuclear DNA content analysis indicated that the genes isolated from M. x giganteus exist in the genome of other Miscanthus species as multiple copies. Analysis of lignin content and histological staining of lignin deposition indicated that higher lignin content is found in mature stem node tissues compared to young leaves and apical stem nodal tissues. Cell wall lignification is associated with increasing tissue maturity in Miscanthus species. RNAi and antisense constructs harboring sequences of these genes were developed to generate Miscanthus transgenic plants with suppressed of lignin biosynthesis and delayed flowering.

Low molecular weight compounds from mushrooms as potential Bcl-2 inhibitors: docking and virtual screening studies

Mushrooms have the ability to promote apoptosis in tumor cell lines, but the mechanism of action is not quite well understood. Inhibition of the interaction between Bcl-2 and pro-apoptotic proteins could be an important step that leads to apoptosis. Therefore, the discovery of compounds with the ability to inhibit Bcl-2 is an ongoing research topic in drug discovery. In this study, we started by analyzing Bcl-2 experimental structures that are currently available in Protein Data Bank database. After analysis of the more relevant Bcl-2 structures, 4 were finally selected. An analysis of the best docking methodology was then performed using a cross-docking and re-docking approach while testing 2 docking softwares: AutoDock 4 and AutoDock Vina. Autodock4 provided the best docking results and was selected to perform a virtual screening study applied to a dataset of 40 Low Molecular Weight (LMW) compounds present in mushrooms, using the selected Bcl-2 structures as target. Results suggest that steroid are the more promising family, among the analyzed compounds, and may have the ability to interact with Bcl-2 and this way promoting tumor apoptosis. The steroids that presented lowest estimated binding energy (ΔG) were: Ganodermanondiol, Cerevisterol, Ganoderic Acid X and Lucidenic Lactone; with estimated ΔG values between -8,45 and -8,23 Kcal/mol. A detailed analysis of the docked conformation of these 4 top ranked LMW compounds was also performed and illustrates a plausible interaction between the 4 top raked steroids and Bcl-2, thus substantiating the accuracy of the predicted docked poses. Therefore, tumoral apoptosis promoted by mushroom might be related to Bcl-2 inhibition mediated by steroid family of compounds.