nils-herrmann/clean_scirepeval huggingface dataset:
Effect of the quorum sensing luxS gene on biofilm formation by Enterococcus faecalis.
Venue: European journal of oral sciences

Enterococcus faecalis is the species of bacterium most frequently isolated from the root canals of teeth that exhibit chronic apical periodontitis refractory to endodontic treatment. In this study, we evaluated the effect of the S ribosylhomocysteine lyase (luxS) quorum sensing gene on E. faecalis biofilm formation by constructing a knockout mutant. The biofilms formed by both E. faecalis and its luxS mutant strain were evaluated using the MTT method. Important parameters that influence biofilm formation, including cell surface hydrophobicity and the nutrient content of the growth medium, were also studied. Biofilm structures were observed using confocal laser scanning microscopy (CLSM) and expression of biofilm related genes was investigated using RT PCR. The results showed that the luxS gene can affect biofilm formation, whereas it does not affect the bacterial growth rate. Deletion of the luxS gene also increased cell surface hydrophobicity. Biofilm formation was accelerated by the addition of increasing concentrations of glucose. The CLSM images revealed that the luxS mutant strain tends to aggregate into distinct clusters and relatively dense structures, whereas the wild type strain appears confluent and more evenly distributed. All genes examined were up regulated in the biofilms formed by the luxS mutant strain. The quorum sensing luxS gene can affect E. faecalis biofilm formation.
Rich Image Captioning in the Wild
Venue: 2016 IEEE Conference on Computer Vision and Pattern Recognition Workshops (CVPRW)

We present an image caption system that addresses new challenges of automatically describing images in the wild. The challenges include generating high quality caption with respect to human judgments, out of domain data handling, and low latency required in many applications. Built on top of a state of the art framework, we developed a deep vision model that detects a broad range of visual concepts, an entity recognition model that identifies celebrities and landmarks, and a confidence model for the caption output. Experimental results show that our caption engine outperforms previous state of the art systems significantly on both in domain dataset (i.e. MS COCO) and out of domain datasets. We also make the system publicly accessible as a part of the Microsoft Cognitive Services.
Faster learning of deep stacked autoencoders on multi core systems using synchronized layer wise pre training
Venue: ArXiv

Deep neural networks are capable of modelling highly non linear functions by capturing different levels of abstraction of data hierarchically. While training deep networks, first the system is initialized near a good optimum by greedy layer wise unsupervised pre training. However, with burgeoning data and increasing dimensions of the architecture, the time complexity of this approach becomes enormous. Also, greedy pre training of the layers often turns detrimental by over training a layer causing it to lose harmony with the rest of the network. In this paper a synchronized parallel algorithm for pre training deep networks on multi core machines has been proposed. Different layers are trained by parallel threads running on different cores with regular synchronization. Thus the pre training process becomes faster and chances of over training are reduced. This is experimentally validated using a stacked autoencoder for dimensionality reduction of MNIST handwritten digit database. The proposed algorithm achieved 26\ speed up compared to greedy layer wise pre training for achieving the same reconstruction accuracy substantiating its potential as an alternative.
Comparative Study of Atorvastatin and Rosuvastatin in Combination with Fenofibrate in mixed Hyperlipidemia

To compare the effects of Atorvastatin and Rosuvastatin in combination with fenofibrate in patients with mixed Hyperlipidemia.  It was an open label, randomized, parallel group, comparative, prospective clinical study. A total of 70 subjects diagnosed with mixed hyperlipidemia were screened and were randomly allocated into two groups of thirty each. Initial readings of lipid levels like TC, TG, HDL, LDL and VLDL for both the groups were taken as baseline values. Then, Group I received Tab Atorvastatin 10 mg Fenofibrate 160 mg and Group II received Tab Rosuvastatin 10 mg+ Fenofibrate 160 mg once a day at night for 12 weeks. Patients were assessed after 12 weeks and their Lipid profile was done.  Patients who received a combination of atorvastatin with fenofibrate had a reduction of Total cholesterol by 39% Triglycerides by 47% LDL C by 50% and VLDL C by 35% respectively. In group treated with combination of rosuvastatin with fenofibrate there was a decrease in TC by 54% TGs by 58% LDL C by 52% and VLDL C by 56% respectively. At the same time, HDL C levels were increased by 14% in the group treated with rosuvastatin with fenofibrate as compared to atorvastatin with fenofibrate treated group which increased the HDL C levels by 6%  Both the treatment regimens significantly decreased TC, TG, LDL C, VLDL C, but the reduction was more and statistically significant in Rosuvastatin and fenofibrate combination group when compared with atorvastatin and fenofibrate treated group at the end of 12 weeks.
Comparison of the safety of statin monotherapy and coadministration with fenofibrate in patients with mixed hyperlipidemia a meta analysis

To compare adverse events of statin monotherapy and combination therapy of statin and fenofibrate.  We searched the online databases of PUBMED and EMBASE for high quality randomized controlled trials (RCTs) Interested outcomes included discontinuation because of any adverse event, any adverse event, serious adverse events, drug related adverse events, increase in alanine aminotransferase (ALT) and/or aspartate aminotransferase (AST) 3 times upper limit of normal (ULN) increase in creatine kinase (CK) 5 times ULN, increase in creatinine 50% and above ULN. As the incidence of adverse events was dichotomous, odds ratios (ORs) were calculated for each included trial with a fixed effects or random effects model depending on the heterogeneity of the studies.  Twelve RCTs covering 5398 participants were included in this meta analysis. Our results revealed that combination therapy was associated with a significantly higher discontinuation because of any adverse event compared with statin monotherapy (P 0.00001) but there were no significant difference in any adverse event (P 0.54) serious adverse events (P 0.55) and drug related adverse events (P 0.39) Fenofibrate plus statin did not result in a greater risk of muscle related adverse events than monotherapy (P 0.79) However, there were more hepatic enzyme elevation related adverse events (P 0.0006) and plasma creatinine elevation related adverse events (P 0.0002) in coadministration group than monotherapy group.  The pooled evidence showed that combination therapy of statin and fenofibrate is associated with a higher incidence of hepatic and renal abnormality compared with statin monotherapy. Fenofibrate should be used carefully in patients with liver and renal impairment, and function of liver and kidney should be monitored closely within the combination therapy.
Development of Acquired Immunity following Repeated Respiratory Syncytial Virus Infections in Cotton Rats
Venue: PloS one

Respiratory syncytial virus (RSV) infections occur every year worldwide. Most infants are infected with RSV by one year of age and are reinfected because immune responses after the first infection are too weak to protect against subsequent infections. In the present study, immune responses against RSV were investigated in order to obtain a better understanding of repetitive RSV infections in cotton rats. No detectable neutralizing antibody (NT) was developed after the first infection, and the second infection was not prevented. The results of histological examinations revealed severe inflammation, viral antigens were detected around bronchial epithelial cells, and infectious viruses were recovered from lung homogenates. Following the second infection neutralizing antibodies were significantly elevated, and CD8+ cells were activated in response to RSV F253 265. No viral antigens was detected thereafter in lung tissues and infectious viruses were not recovered. Similar results were obtained in the present study using the subgroups A and B. These results support the induction of humoral and cellular immune responses following repetitive infections with RSV; however, these responses were insufficient to eliminate viruses in the first and second infections.
The Effects of Risk Perceptions and Liquidity Constraints on the Storage Decisions of Maize and Legume Producers in Uganda

This study empirically investigates the effects of risk perceptions and liquidity constraints on the maize and legume storage decisions in Uganda. Maize is the most important staple food in Eastern and Southern Africa, and legume crops constitute the major source of protein for most of these consumers. While production is seasonal, consumption occurs year round. As a result, postharvest storage decisions among smallholder farmers are important for food and income security. We use a randomized control trial implemented among more than 1000 farm households to study how perceptions of postharvest losses through improved storage technology, and cash saving at the beginning of harvest, influence storage decisions. We exogenously treated one group of farm households by providing them with improved storage technology. A control group continued to use traditional storage techniques. Preliminary investigation suggests that for maize, an expected loss of 1kg increased quantity stored by about 1kg. Households with cash on hand at the beginning of harvest increased storage by 60kgs. For legume crops, households store 2.5kg more when anticipating similar storage losses and 24kgs more when they possess cash savings at the beginning of harvest.
The Hare and the Fast Tortoise: Dynamic Resource Reconfiguration and the Pursuit of New Growth Opportunities by Yahoo and Google (1995 2007)

Strategic management research has shown growing interest in understanding the dynamic resource reconfiguration processes through which firms grow, evolve, and sustain profitability. The goal of our study is to understand how dynamic resource reconfigurations enable firms to pursue growth opportunities. We use the methods of inductive theory building from case studies to elaborate current theoretical understanding about how firms draw on both internal and external resources in the pursuit of growth. We examine the patterns of resource reconfigurations through which Yahoo and Google powered their early growth strategies in their first 10 years of existence. We analyze a total of 192 new product launches in 43 markets by the two firms to capture how they reconfigured resources dynamically. Our analysis reveals that both firms developed highly dynamic strategies exhibiting both surprising similarities and differences. These similarities and differences provided the basis for our theoretical insights about the development of what we term "dynamic resource platforms," comprising of (a) dynamic resource shifts; (b) targeted resource orchestration; and (c) complementary processes balancing dynamism and capability development. These ideas contribute novel theoretical insights to current strategic management research on dynamic capabilities and on resource reconfiguration and redeployment.
Foods contributing to vitamin B6, folate, and vitamin B12 intakes and biomarkers status in European adolescents: The HELENA study
Venue: European Journal of Nutrition

PurposeTo examine the association between food groups consumption and vitamin B6, folate and B12 intakes and biomarkers in adolescents.MethodsIn total 2189 individuals participating in the cross sectional Healthy Lifestyle in Europe by Nutrition in Adolescence study met the eligibility criteria for analysis of dietary intakes (46 males) and 632 for biomarker analysis (47 males) Food intakes were assessed by two non consecutive 24 h recalls. Biomarkers were measured by chromatography and immunoassay. Food groups which best discriminated participants in the extreme tertiles of the distribution of vitamins were identified by discriminant analyses. Food groups with standardised canonical coefficients higher or equal to 0.3 were selected as valid discriminators of vitamins intake and biomarkers extreme tertiles. Linear mixed model elucidated the association between food groups and vitamins intakes and biomarkers.ResultsVitamin B6 intakes and biomarkers were best discriminated by meat (males and females) margarine and mixed origin lipids only in males and breakfast cereals (females) Breakfast cereals (males) and fruits, margarine and mixed origin lipids, vegetables excluding potatoes, breakfast cereals, and soups/bouillon (females) determined the most folate intakes and biomarkers. Considering vitamin B12 intakes and biomarkers, meat, and white and butter milk (males and females) snacks (males) and dairy products (females) best discriminated individual in the extremes of the distribution. Fewer associations were obtained with mixed model for biomarkers than for vitamins intakes with food groups.ConclusionsWhereas B vitamin intakes were associated with their food sources, biomarkers did with overall food consumption. Low nutrient density foods may compromise adolescents' vitamin status.
A CONTRIBUICAO DA FISIOTERAPIA NOS CUIDADOS PALIATIVOS EM CRIANCAS COM LEUCEMIA

Este artigo teve como objetivo apontar as principais acoes do fisioterapeuta nos cuidados paliativos para o restabelecimento da qualidade de vida da crianca com leucemia. Este estudo apresenta carater teorico, exploratorio com abordagem qualitativa. Atraves dos resultados obtidos a fisioterapia pode ser benefica nos cuidados paliativos de criancas com leucemia, pois conta com um arsenal extenso de tecnicas como a cinesioterapia, eletroterapia e hidroterapia que possibilitam ao paciente passar menos tempo hospitalizado e mais tempo com a familia e amigos.
Desvelando a experiencia de maes de criancas com cancer em uma unidade de cuidados paliativos

Objetivo: compreender o cotidiano de maes cuidadoras de criancas com cancer. Metodologia: pesquisa descritiva, com abordagem qualitativa realizada em uma unidade de cuidados paliativos de um Hospital de Ensino, no Nordeste do Brasil, com 20 maes. Para a selecao das participantes adotou se os seguintes criterios de inclusao que tivessem maiores de 18 anos; que estivessem acompanhando seu filho na instituicao; Os dados foram coletados por meio de uma entrevista semiestruturada e analisados a partir das bases conceituais do Discurso do Sujeito Coletivo. Resultados Os relatos das maes foram categorizados em tres topicos " Mudancas no cotidiano familiar" " Mudancas na vida pessoal" e " Restricao na vida social" As mudancas na vida profissional, familiar e pessoal, foram: o abandono do emprego, o afastamento do lar e de suas funcoes domesticas, deixando conjuge e outros filhos a propria sorte, o desprendimento de seus desejos e necessidades pessoais. Conclusao a vida de maes de criancas com cancer foi marcada por mudancas importantes na rotina familiar, motivadas pela necessidade de dedicar integralmente aos cuidados do filho
Color Discrimination Is Affected by Modulation of Luminance Noise in Pseudoisochromatic Stimuli
Venue: Front. Psychol.

Pseudoisochromatic stimuli have been widely used to evaluate color discrimination and to identify color vision deficits. Luminance noise is one of the stimulus parameters used to ensure that subject's response is due to their ability to discriminate target stimulus from the background based solely on the hue between the colors that compose such stimuli. We studied the influence of contrast modulation of the stimulus luminance noise on threshold and reaction time color discrimination. We evaluated color discrimination thresholds using the Cambridge Color Test (CCT) at six different stimulus mean luminances. Each mean luminance condition was tested using two protocols: constant absolute difference between maximum and minimum luminance of the luminance noise (constant delta protocol, CDP) and constant contrast modulation of the luminance noise (constant contrast protocol, CCP) MacAdam ellipses were fitted to the color discrimination thresholds in the CIE 1976 color space to quantify the color discrimination ellipses at threshold level. The same CDP and CCP protocols were applied in the experiment measuring RTs at three levels of stimulus mean luminance. The color threshold measurements show that for the CDP, ellipse areas decreased as a function of the mean luminance and they were significantly larger at the two lowest mean luminances, 10 cd/m2 and 13 cd/m2, compared to the highest one, 25 cd/m2. For the CCP, the ellipses areas also decreased as a function of the mean luminance, but there was no significant difference between ellipses areas estimated at six stimulus mean luminances. The exponent of the decrease of ellipse areas as a function of stimulus mean luminance was steeper in the CDP than CCP. Further, reaction time increased linearly with the reciprocal of the length of the chromatic vectors varying along the four chromatic half axes. It decreased as a function of stimulus mean luminance in the CDP but not in the CCP. The findings indicated that visual performance using pseudoisochromatic stimuli was dependent on the Weber's contrast of the luminance noise. Low Weber's contrast in the luminance noise is suggested to have a reduced effect on chromatic information and, hence, facilitate desegregation of the hue defined target from the background.
Juicebox Provides a Visualization System for Hi C Contact Maps with Unlimited Zoom.
Venue: Cell systems

Hi C experiments study how genomes fold in 3D, generating contact maps containing features as small as 20 bp and as large as 200 Mb. Here we introduce Juicebox, a tool for exploring Hi C and other contact map data. Juicebox allows users to zoom in and out of Hi C maps interactively, just as a user of Google Earth might zoom in and out of a geographic map. Maps can be compared to one another, or to 1D tracks or 2D feature sets.
Herbal Medicines for the Management of Irritable Bowel Syndrome: A Systematic Review
Venue: Electronic physician

Irritable Bowel Syndrome (IBS) is a chronic digestive disorder, which is characterized by abdominal pain, bloating, diarrhea and constipation periods. The etiology is unknown. Based on the different mechanisms in the etiology, treatment focuses on controlling symptoms. Due to the longtime of syndrome, inadequacy of current treatments, financial burden for patients and pharmacologic effects, several patients have turned to the use of complementary and alternative medicine (CAM) Complementary and alternative treatments for IBS include hypnosis, acupuncture, cognitive behavior therapy, yoga, and herbal medicine. Herbal medicines can have therapeutic effects and adverse events in IBS. The aim of this study was to evaluate the efficacy of herbal medicines in the control of IBS, and their possible mechanisms of action were reviewed. Herbal medicines are an important part of the health care system in many developing countries It is important for physicians to understand some of the more common forms of CAM, because some herbs have side effects and some have interactions with conventional drugs. However herbal medicines may have therapeutic effects in IBS, and further clinical research is needed to assess its effectiveness and safety.
Performance Responses, Nutrient Digestibility, Blood Characteristics, and Measures of Gastrointestinal Health in Weanling Pigs Fed Protease Enzyme
Venue: Asian Australasian journal of animal sciences

Although exogenous protease enzymes have been used in poultry diets quite extensively, this has not been the case for pig diets. In general, due to their better gut fermentative capacity and longer transit time, pigs have greater capacity to digest dietary proteins than poultry. However, in early weaned piglets, the stress brought about by weaning adversely affects the digestion of dietary proteins. Therefore, a study was conducted to determine the effects of a commercial protease enzyme in weanling pigs. Indices of growth, nutrient digestibility, blood profiles, fecal microflora, fecal gas emission and fecal scores were measured during the study. A total of 50 weanling pigs (6.42+ 0.12 kg) at 28 d of age were randomly assigned to receive 1 of 2 dietary treatments: i) control diet (corn soy based) with no supplemental protease (CON) and ii) control diet+200 g/ton protease (PROT) for 42 d. A completely randomized design consisting of 2 treatments, 5 replicates, and 5 pigs in each replicate was used. Growth performance in terms of body weight (27.04+ 0.38 kg vs 25.75+ 0.39 kg; p<0.05) and average daily gain (491+ 7.40 g vs 460+ 7.46 g; p<0.05) in PROT fed pigs were increased significantly, but gain per feed (0.700+ 0.01 vs 0.678+ 0.01; p>0.05) was similar between treatments at d 42. Relative to CON pigs, PROT fed pigs had increased (p<0.05) apparent total tract digestibility (84.66% 0.65% vs 81.21% 1.13% dry matter and 84.02% 0.52% vs 80.47% 1.22% nitrogen) and decreased (p<0.05) NH3 emission (2.0+ 0.16 ppm vs 1.2+ 0.12 ppm) in the feces at d 42. Except for a decreased (p<0.05) in blood creatinine level, no differences were observed in red blood cell, white blood cell, lymphocyte, urea nitrogen, and IgG concentrations between treatments. Fecal score and fecal microflora (Lactobacillus and E. coli) were also similar between CON and PROT groups. Overall, the supplementation of protease enzyme in weanling pigs resulted in improved growth rate and nutrient digestibility. Exogenous protease enzyme reduced fecal NH3 emission, thus, potentially serving as a tool in lowering noxious gas contribution of livestock production in the environment.
Thermotolerant alkaline protease enzyme from Bacillus licheniformis A10: purification, characterization, effects of surfactants and organic solvents
Venue: Journal of enzyme inhibition and medicinal chemistry

In this study, the extracellular thermostable alkaline protease out of A10 strain was purified 1.38 fold with 9.44% efficiency through the ammonium sulfate precipitation dialysis and DE52 anion exchange chromatography methods. The molecular weight of the enzyme in question along with sodium dodecyl sulfate polyacrylamide gel electrophoresis was determined to be approximately 40.55 kDa, whereas the optimum pH and temperature ratings were identified as 9.0 and 70 degC, respectively. It was seen that the enzyme had remained stable between pH 7.5 10.5 range, protecting more than 90% of its activity in the wake of 1 h incubation at 60 70 degC. It was also observed that the enzyme enhanced its activity in the presence of Mg2+ Mn2+ K+ while Fe2+ Ni2+ Zn2+ Ag+ and Co2+ decreased the activity. Ca2+ however, did not cause any change in the activity. The enzyme was seen to have been totally inhibited by phenylmethylsulfonyl fluoride, therefore, proved to be a serine alkaline protease.