bluuebunny/crossref_metadata_2025 huggingface dataset:
The 10-Year Incidence Trend of Common Cancers at a Referral Hospital in Tehran, Iran From 2007 to 2016
Authors: Sanaeinasab Hormoz , Davoudi Monfared Esmat , Karimi Zarchi Ali-Akbar , Saffari Mohsen , Delavari Abdowreza
Published: October 2019

Background: Common cancers such as colon, breast, and lung cancer are increasing in developing countries. Objective: This study was conducted to determine 10-year trends and changes in common cancers in patients from a referral hospital in Tehran, Iran. Methods: This cross-sectional study investigated a study population comprising colon, stomach, lung, prostate, and breast cancer patients registered at the cancer center of a referral hospital in Tehran, Iran from April 1, 2007 to the end of March, 2016 (n=4472). Inclusion criteria were a definitive diagnosis of cancer and an age between 15 and 75 years. Data was entered into SPSS (version 18) software and analyzed using the Time Series analysis and Scatter IO graph. Results: Significant correlations (P value <0.001) were seen between age increases in patients and the increasing number of patients in any type of cancer. With almost all of the five studied cancers, incidence increased with aging (P value <0.001). The incremental linear trend in the age of patients with lung (P value = 0.008) and colon (P value = 0.004) cancers and the decreasing trend in the age of prostate cancer patients (P value = 0.001) were statistically significant. Conclusion: The incidence of cancer has increased over the past 10 years in both genders and ages. It is suggested that future studies should address the causes and factors behind the increasing incidence of common cancers.
What Happens When Donors Pull Out? Examining Differences in Motivation Between Health Workers Who Recently Had Performance-Based Financing (PBF) Withdrawn With Workers Who Never Received PBF in the Democratic Republic of Congo
Authors: Maini Rishma , Lohmann Julia , Hotchkiss David R. , Mounier-Jack Sandra , Borghi Josephine
Published: October 2019

Background: A motivated workforce is necessary to ensure the delivery of high quality health services. In developing countries, performance-based financing (PBF) is often employed to increase motivation by providing financial incentives linked to performance. However, given PBF schemes are usually funded by donors, their long-term financing is not always assured, and the effects of withdrawing PBF on motivation are largely unknown. This cross-sectional study aimed to identify differences in motivation between workers who recently had donor-funded PBF withdrawn, with workers who had not received PBF. Methods: Quantitative data were collected from 485 health workers in 5 provinces using a structured survey containing questions on motivation which were based on an established motivation framework. Confirmatory factor analysis was used to verify dimensions of motivation, and multiple regression to assess differences in motivation scores between workers who had previously received PBF and those who never had. Qualitative interviews were also carried out in Kasai Occidental province with 16 nurses who had previously or never received PBF. Results: The results indicated that workers in facilities where PBF had been removed scored significantly lower on most dimensions of motivation compared to workers who had never received PBF. The removal of the PBF scheme was blamed for an exodus of staff due to the dramatic reduction in income, and negatively impacted on relationships between staff and the local community. Conclusion: Donors and governments unable to sustain PBF or other donor-payments should have clear exit strategies and institute measures to mitigate any adverse effects on motivation following withdrawal.
Personality, Schizophrenia, and Violence: A Longitudinal Study: The Second Wave of the VIORMED Project
Authors: Bottesi Gioia , Candini Valentina , Ghisi Marta , Bava Mattia , Bianconi Giorgio , Bulgari Viola , Carrà Giuseppe , Cavalera Cesare , Conte Giovanni , Cricelli Marta , Ferla Maria Teresa , Iozzino Laura , Macis Ambra , Stefana Alberto , de Girolamo Giovanni ,   the VIORMED-2 Group
Published: October 2019

This study investigated the association between maladaptive personality traits, personality disorders (PDs), schizophrenia, and the risk of aggressive behavior. Ninety-four patients with a history of violence and 92 patients with no history of violence underwent a multidimensional baseline assessment. Aggressive behavior was monitored during a 1-year follow-up through the Modified Overt Aggression Scale. The Violent group scored significantly higher than the Control group on the Millon Clinical Multiaxial Inventory (MCMI-III) Antisocial, Sadistic, Borderline, and Paranoid personality scales. Irrespective of any history of violence, patients with PD as a primary diagnosis displayed more aggressive behaviors than those with a primary diagnosis of schizophrenia during the follow-up. Furthermore, the most significant predictor of aggressive behaviors over time was endorsing a primary diagnosis of PD. Identifying the crucial risk factors for violent recidivism would contribute to reducing aggressive behavior in this population.
Effect of Psychotherapy for Borderline Personality Disorder on Quality of Life: A Systematic Review and Meta-Analysis
Authors: Chakhssi Farid , Zoet J. Monique , Oostendorp Jeanine M. , Noordzij Matthijs L. , Sommers-Spijkerman Marion
Published: October 2019

Whereas several meta-analyses have shown that psychotherapy is effective for reducing borderline personality disorder (BPD) pathology, the overall impact of psychotherapy for BPD on quality of life (QoL) remains as yet unclear. Because impaired QoL is associated with poor long-term outcomes after therapy for BPD, this seems a timely and relevant issue. The authors conducted a systematic review and meta-analysis of randomized controlled trials of psychotherapies for adults diagnosed with BPD that reported results of QoL at posttreatment. Fourteen trials were included (1,370 individuals with BPD). Psychotherapies for BPD relative to control conditions showed significant effect sizes for QoL (Cohen's d = 0.31; 95% CI [0.18, 0.44]), and for BPD pathology (d = 0.43; 95% CI [0.23, 0.64]). The effect on QoL was not significantly moderated by the effect on BPD pathology. Psychotherapies for BPD have a positive effect on QoL of patients with BPD. However, more studies are needed to examine the impact of psychotherapy on QoL and long-term outcome, including recovery.
Perceived Caretaker Malevolence During Childhood Reported by Borderline Patients and Personality-Disordered Comparison Subjects: Description and Prediction
Authors: Ridolfi Maria E. , Temes Christina M. , Fraser Emily K. , Frankenburg Frances R. , Zanarini Mary C.
Published: October 2019

This study has two purposes. The first is to assess the rates of childhood malevolence by caretakers reported by a well-defined sample of inpatients with borderline personality disorder (BPD) and comparison subjects with other personality disorders. The second purpose is to determine the relationship between reported malevolence of caretakers and possible risk factors for this experience. Two reliable interviews were administered to 290 borderline inpatients and 72 personality-disordered comparison subjects to address these aims. Malevolence was reported by a significantly higher percentage of borderline patients than comparison subjects (58% vs. 33%). In multivariate analyses, severity of other forms of abuse, severity of neglect, and a family history of a dramatic cluster personality disorder were found to significantly predict perceived malevolence. Taken together, the results of this study suggest that experiencing malevolence is common and distinguishing for BPD, and that the risk factors for reported childhood malevolence are multifactorial in nature.
Presença da família durante o atendimento emergencial pré-hospitalar: percepção e vivência dos profissionais
Authors: Cruz Jéssica Fernanda Maniezo da , Gomes João Rogério Zequim , Barreto Mayckel Da Silva , Marcon Sonia Silva
Published: October 2019

Objetivo: compreender como profissionais do Serviço de Atendimento Móvel às Urgências vivenciam e percebem a presença da família durante o atendimento pré-hospitalar. Método: pesquisa qualitativa, realizada em um município do norte do Paraná. Os dados foram coletados entre junho e agosto de 2018, com 12 profissionais, por meio de entrevistas semiestruturadas, gravadas, transcritas e analisadas conforme a Análise de Conteúdo, modalidade temática. Resultados: identificou-se que poucos profissionais estavam dispostos a permitir a presença das famílias, pois acreditavam que elas poderiam atrapalhar a assistência e sofrer com as cenas produzidas pelo atendimento. Aqueles que percebiam a presença familiar como positiva, entendiam que os familiares se configuravam como fonte de informação sobre o paciente e o cenário assistencial. Considerações finais: é necessário que estratégias de sensibilização sejam realizadas junto aos profissionais para que possam perceber a família não apenas como fonte de informação, mas também como parte integrante da assistência.
Fast, Flexible Closed-Loop Feedback: Tracking Movement in “Real-Millisecond-Time”
Authors: Sehara Keisuke , Bahr Viktor , Mitchinson Ben , Pearson Martin J. , Larkum Matthew E. , Sachdev Robert N. S.
Published: October 2019

One of the principal functions of the brain is to control movement and rapidly adapt behavior to a changing external environment. Over the last decades our ability to monitor activity in the brain, manipulate it while also manipulating the environment the animal moves through, has been tackled with increasing sophistication. However, our ability to track the movement of the animal in real time has not kept pace. Here, we use a dynamic vision sensor (DVS) based event-driven neuromorphic camera system to implement real-time, low-latency tracking of a single whisker that mice can move at ∼25 Hz. The customized DVS system described here converts whisker motion into a series of events that can be used to estimate the position of the whisker and to trigger a position-based output interactively within 2 ms. This neuromorphic chip-based closed-loop system provides feedback rapidly and flexibly. With this system, it becomes possible to use the movement of whiskers or in principal, movement of any part of the body to reward, punish, in a rapidly reconfigurable way. These methods can be used to manipulate behavior, and the neural circuits that help animals adapt to changing values of a sequence of motor actions.
A Century of Contention in South Korea
Authors: Stent Dylan
Published: October 2019

This paper examines a century of contentious politics in South Korea. I argue that there have been three distinctive eras of contention in modern Korea. The first two eras saw institutional arrangements limit the success of contentious campaigns. However, expanded repertoires in the third era allowed movements to succeed. I end by examining the role of social media in future movements.
Conservative Politics and Compassionate Paternalism in Korea and Japan
Authors: Yun Ji-Whan
Published: October 2019

It is widely predicted that East Asia’s conservative governments will lose political power for managing socioeconomic crises under neoliberal globalization and find no way out of their legitimacy problem. However, Korea’s and Japan’s conservative governments have recently constructed a new model of crisis management—compassionate paternalism—in a highly discretionary manner.
Can technology save the environment? Lessons from Iain M. Banks’ Culture series
Authors: Nicholson Simon
Published: October 2019

A common theme in speculative fiction concerns technological overreach. All manner of scenarios have been developed by science fiction authors and filmmakers, warning of the potential for subjugation, obliteration, or alienation as technologies grow in power and scale. Yet within environmental circles, even though the dangers inherent in technological development are well appreciated, environmental challenges are coming to be defined more and more as technical matters to be resolved via technological means. This article explores some of the meaning and limits of this contemporary environmental techno-optimism, through engagement with the “Culture” novels of Iain M. Banks. The Culture novels chronicle a space-faring, post-scarcity civilization, and stand as a kind of best-case extension, in environmental terms, of humanity’s present technological trajectory. The article wrestles with the potential for great benefit but also extraordinary risk that comes with treading down Banks’ path and outlines the kinds of questions that must be asked and answered in an increasingly technology-saturated world. The article distills lessons from comparing Banks’ novels to the “Biosphere 2” experiment. It also explores a few of the ways in which speculative fiction might be deployed in the classroom to better equip students and citizens to wrestle with existing and emerging technologies and their implications.
Analysis of calpastatin and сallipyge genes polymorphism in Prydniprovska meat sheep
Authors: Pomitun I. , Rossokha V. , Boyko Ye. , Guzevatyi O. , Shpilka M. , Kulibaba R.
Published: October 2019

Aim. To study calpastatin (CAST) and сallipyge (CLPG) genes polymorphism in Prydniprovska meat sheep. Methods. The studies were conducted using PCR-RFLP method. DNA was isolated from 47 animals. The amplicons were treated with restriction endonucleases MspI and FaqI for genes CAST and CLPG, respectively. Results. The study determined the polymorphism of CAST gene fragment. Two alleles – M (336, 286 b.p.) and N (622 b.p.) with the frequency of 0.83 and 0.17, respectively, were detected. The frequency of genotypes was as follows: ММ – 0.77, MN – 0.13 and NN – 0.10. There was a noted tendency towards the increase in live bodyweight of 4-month-old lambs, carriers of N allele (genotypes NN and MN), compared to the index for the lambs of the same age with genotype MM. Locus CLPG was monomorphic, only allele A was determined (278, 117 and 31 b.p.). Allele G with the mutation, manifested in muscle hypertrophy phenotype, was not detected, all the animals under investigation had genotype AA. Conclusions. CAST gene
polymorphism was deter- mined in Prydniprovska meat sheep during our work. The tendency towards the increase in live bodyweight of 90-day-old lambs, carriers of allele N, was established which demonstrated promising perspectives of further studies on associations of this gene and meat qualities of Prydniprovska meat sheep. The obtained results on the monomorphic nature of locus CLPG and the absence of mutation, related to muscle hypertrophy phenotype, demonstrated that the mutation of this gene may be built into the genome of domestic breeds of sheep only via cross-breeding with foreign breeds, in which this trait is manifested.
KINERJA MANAJER INVESTASI REKSADANA SAHAM SYARIAH DI INDONESIA
Authors: ANITA ANITA
Published: October 2019

The purpose of this study is to test the ability of investment managers in Islamic mutual funds in their ability to conduct stock selection and market timing. The model developed in this study uses the Henriksson-Merton model. With purposive sampling technique obtained a sample of 31 mutual funds. After testing the results obtained, the performance of Islamic stock mutual funds in Indonesia underperformed compared to the ISSI market performance. The stock selection results contribute negatively to α = 5%, while the ability of market timing has a significant positive effect on mutual fund returns.
The Ancient Hydraulic Infrastructure of Wādi eṣ-Ṣader near Petra, Southern Jordan
Authors: Al-Salameen Adeeb , Al-Salameen Zeyad , Falahat Hani
Published: October 2019

Intensive investigations of the archaeological remains at agricultural sites and water springs may provide a wealth of information. The remains, recently revealed in the vicinity of eṣ-Ṣader spring3, inspired the authors to investigate the area in and around Wādī eṣ-Ṣader. These explorations have enhanced our knowledge about the importance of this spring in the lives of the inhabitants of Wādī Moūsā as early as the Nabataean period. The existing archaeological evidence in this region, which will be discussed in this paper, includes remains of Nabataean terracotta water pipelines as well as Islamic water mills. In addition, the paper includes a discussion on some of the ancient toponyms either mentioned in the Petra archive and other place names which are of Aramaic origin. The latter indicates that these were used when Aramaic was the lingua franca in the region during the Nabataean period. Additionally, the inherited water traditions in the study area are presented in an attempt to trace their historical origin. Finally, the importance of terrace cultivation in this region through ages is also highlighted.
The Derivation of the Tibetan Present Prefix g- from ḥ-
Authors: Hill Nathan W.
Published: October 2019

According to the communis opinio it is arbitrary whether a Tibetan verb takes the prefix g- or ḥ- in its present stem. This paper instead argues that ḥ- [ɣ] originated as a phonetically conditioned variant of g-; a pattern that became obscured through the coinage of denominative verbs and analogical developments.
First record of Wild Boar (Sus scrofa Linnaeus, 1758) in Lençóis Maranhenses National Park, Maranhão state, northern Brazil
Authors: Salvador Gilberto Nepomuceno , Garcia Ristau Nathali , Sanches da Silva Isabel , Nunes André Valle
Published: October 2019

The Wild Boar is one of the world’s most dangerous invasive species. It is now established in many regions beyond its native range, including many Brazilian states. However, the species has never been recorded from the Brazilian state of Maranhão. Here, we report the first occurrence of this species from Lençóis Maranhenses National Park, within the municipality of Barrerinhas, Maranhão state. We discuss the negative effects of this introduction on native species, including the problem with predation of nests of an endangered turtle species by Wild Boar.
On the coupled, flexural−flexural−torsional vibrations of an asymmetric concrete beam
Authors: Karadelis John N.
Published: October 2019

This paper presents the analytical solution of an L-shaped cross-section asymmetric beam (concrete terrace unit) undergoing ‘triple coupling’, that is, flexural vibration in two mutually perpendicular planes (vertical and horizontal) plus torsional vibration about an axis passing through its shear centre, using the classical approach. Essentially, the procedure involved the development of three governing, coupled, partial differential equations based on Euler–Bernoulli theory for beams with isotropic material properties, from which the ‘exact’ solution was extracted. The warping effect was considered in the torsional equation. A comparison between the analytical solution and corresponding numerical and experimental results obtained earlier was attempted, and similarity and accuracy were discussed. It is reasonable to state that the analytical method in calculating the natural frequencies of a system is the most reliable, compared to experimental (needs, skills and experience) and numerical (calibration, updating, validation etc.). However, even the analytical solution may not be as accurate as expected, as it depends on several factors/parameters beyond the full control of the investigator. Some useful comments and conclusions are drawn.
Long-Term Outcomes of Arteriovenous Fistulas with Unassisted versus Assisted Maturation: A Retrospective National Hemodialysis Cohort Study
Authors: Lee Timmy , Qian Joyce Zhang , Zhang Yi , Thamer Mae , Allon Michael
Published: October 2019

Significance Statement

Before successful use in dialysis, many arteriovenous fistulas (AVFs) require one or more endovascular or surgical interventions to assist clinical maturation. However, the effect of assisted maturation on long-term postmaturation AVF outcomes is poorly studied. In this retrospective analysis, the authors analyzed the US Renal Data System to identify elderly patients who underwent AVF creation after initiation of hemodialysis, and whose AVF was used successfully for dialysis with or without assisted maturation. Their analysis of the relationship between the number of prematuration AVF interventions and postmaturation AVF outcomes found a positive association between the number of prematuration interventions and the likelihood of primary patency loss and frequency of interventions after maturation. These findings highlight the high burden of costly interventions to assist clinical maturation for successful AVF use.

Background

About half of arteriovenous fistulas (AVFs) require one or more interventions before successful dialysis use, a process called assisted maturation. Previous research suggested that AVF abandonment and interventions to maintain patency after maturation may be more frequent with assisted maturation versus unassisted maturation.

Methods

Using the US Renal Data System, we retrospectively compared patients with assisted versus unassisted AVF maturation for postmaturation AVF outcomes, including functional primary patency loss (requiring intervention after achieving AVF maturation), AVF abandonment, and frequency of interventions.

Results

We included 7301 patients ≥67 years who initiated hemodialysis from July 2010 to June 2012 with a catheter and no prior AVF; all had an AVF created within 6 months of starting hemodialysis and used for dialysis (matured) within 6 months of creation, with 2-year postmaturation follow-up. AVFs matured without prior intervention for 56% of the patients. Assisted AVF maturation with one, two, three, or four or more prematuration interventions occurred in 23%, 12%, 5%, and 4% of patients, respectively. Patients with prematuration interventions had significantly increased risk of functional primary patency loss compared with patients who had unassisted AVF maturation, and the risk increased with the number of interventions. Although the likelihood of AVF abandonment was not higher among patients with up to three prematuration interventions compared with patients with unassisted AVF maturation, it was significantly higher among those with four or more interventions.

Conclusions

For this cohort of patients undergoing assisted AVF maturation, we observed a positive association between the number of prematuration AVF interventions and the likelihood of functional primary patency loss and frequency of postmaturation interventions.
A Study on the Effectiveness of Airline Safety VR Education: Focusing on the Relations Safety VR Education, Emotional Immersion and Safety Behavior
Authors:   The Tourism Sciences Society Of Korea, Park Hee-Jung
Published: October 2019

This study was conducted in May 2019 with J-Air cabin crew members who had participated in safety VR education for one month to check the impact of safety VR education on emotional immersion and safety behavior and to provide implications for how to use safety VR education programs by verifying the mediation effects of emotional immersion in the relationship between safety VR education and safety behavior. First, the results of checking how safety VR education affected emotional immersion demonstrated that the three factors (the suitability of the educational environment for safety VR education, response ability to safety accidents, and attitude of participation in education) all had a significant positive influence on emotional immersion. Also, among them, suitability of educational environment for safety was the most important factor. Therefore, in carrying out safety training for cabin crew members, airlines need to reorganize the safety education program by applying a VR education system and by presenting the same visual contents that actual airlines use, including symbols, airline uniforms, and airline cabin structures of the aircraft used in the safety VR training. In addition, the results of demonstrating the impact of safety VR education on safety behavior showed that all three factors had a significant positive influence on safety behavior, with the most important being education participation. Therefore, in organizing safety VR education, airlines need to implement vocational training first. In addition, as a result of checking the effect of emotional immersion on safety, it had a significant positive influence on safety action. Therefore, airlines should rearrange the composition of safety VR education centers so that three to four cabin crew members can receive safety VR education in separate spaces using a partition. Finally, after analyzing whether the impact relationship between safety VR education and safety behavior was mediated by emotional immersion, it was demonstrated that there was a partial mediating effect in the relationship. The government should expand safety VR education, which is currently used only by J-Air, to all airlines in Korea and expand the number of people who participate in it to all jobs linked to air operations. Airlines also need to develop safety VR education programs focusing on customer safety accidents that suit the specificity of the cabin crews’ in-flight security tasks.
Image-based 3D cell culture cytotoxicity assay v1
Authors: Gottschalk Elinor , Arman Aksoy Bulent , Aksoy Pinar , Czech Eric , Hammerbacher Jeff
Published: October 2019

This protocol describes an imaged-based 3-dimensional (3D) cell culture cytotoxicity assay using multicellular tumor spheroids (in this case MC38 cells) sensitized with hgp100 peptide and killing them with pmel-1 T cells or the apoptosis-inducing antibiotic, Staurosporine. Our goal was to explore an in vitro 3D cell culture system to study T cell-mediated cytotoxicity as a potential way to more rapidly and relevantly test the effect of T cell manipulation on T cell cytotoxicity before moving to the mouse model. In this setup, the T cells are required to migrate towards the tumor spheroids that are already suspended in a gel matrix, there is minimal manipulation of the samples post-coculture because the samples are imaged directly in the chips to measure cell death, and there is somewhat higher throughput than confocal imaging provides (more spheroids being imaged per sample via widefield microscopy). We used 3D cell culture chips from AIM Biotech (Singapore) and adapted protocols published by: AIM Biotech: https://www.aimbiotech.com/general-protocols.html Pavesi, Andrea, Anthony T. Tan, Sarene Koh, Adeline Chia, Marta Colombo, Emanuele Antonecchia, Carlo Miccolis, et al. 2017. “A 3D Microfluidic Model for Preclinical Evaluation of TCR-Engineered T Cells against Solid Tumors.” JCI Insight 2 (12). https://doi.org/10.1172/jci.insight.89762. Jenkins, Russell W., Amir R. Aref, Patrick H. Lizotte, Elena Ivanova, Susanna Stinson, Chensheng W. Zhou, Michaela Bowden, et al. 2018. “Ex Vivo Profiling of PD-1 Blockade Using Organotypic Tumor Spheroids.” Cancer Discovery 8 (2): 196–215. For image analysis, refer to: Czech, Eric, Bulent Arman Aksoy, Pinar Aksoy, and Jeff Hammerbacher. 2019. “Cytokit: A Single-Cell Analysis Toolkit for High Dimensional Fluorescent Microscopy Imaging.” BMC Bioinformatics 20 (1): 448.
IPTG-induced Overexpression in E. coli v1
Authors: Dusseldorf Igem
Published: October 2019

LB 1M IPTG BPER HEPES Protein Expression (optimised for inclusion bodies) Take volume (100ml) LB+ Ampicillin Add 1 ml of the over night culture Let the culture grw to an OD of 0.6 at 37°/180 rpm Induce with 0,5 mM IPTG (1M Stock) --> 50 µl Incubate for 2 hours at 37°/ 180 rpm Centrifuge the culture for 10 minutes at 4000xg / 4°C Store Pellet without supernatant at -80° Purification of inclusion bodies Thaw cell pellet on ice Resuspend Pellet in 1 ml Water (2x50ml Pellets from 100ml culture can be resuspended together) Transfer to 2 ml Eppis Centrifuge at maximum speed of a desktop centrifuge at 4°C for 15 minutes Discard supernatant Resuspend Pellet in 0,5 ml BPER by vortexting Repeat vortexing every 2 minutes for 15 minutes Centrifuge at maximum speed of a desktop centrifuge at 4°C for 15 minutes Store the supernatant (BPER) in seperate Eppis (on ice) Dilute 1 ml BPER with 9 ml Water to create 1/10 BPER Wash the pellet with 1 ml 1/10 BPER (can be done by vortexing for 3x1 minute) Centrifuge at maximum speed of a desktop centrifuge at 4°C for 15 minutes Store the supernatant (1/10 BPER) in seperate Eppis (on ice) Resuspend Pellet in 200 μl 50 mM HEPES pH7.4, 150 mM KCl, 10% Glycerol (If you do not intend to use your protein for activity assays, Water can also be used) Put samples on SDS-Gel or store at -20°C. On an SDS-Gel mix 0,5-1µl of sample + 4 µl 5xSDS-Buffer and put on the gel
Western Blot (Tank-Blot) v1
Authors: Dusseldorf Igem
Published: October 2019

Blotting Buffer: 100mL 10x SDS running buffer 200mL 100% Methanol 700mL H20 Fill a tray with blotting buffer Transfer SDS gel to the blotting buffer Assemble blotting sandwich (take it, soak sponge and place on it, soak filter paper and place on it, place inverted SDS gel on top, without creating bubbles.Add charged PDVF membrane with forceps ( charged in 100% ethanol and then soaked in buffer ) Add soaked filter Streak out bubbles Add soaked sponge Press together and close container Place in blotting apparatus and add lotting buffer Run for 1h at 100V 350-500mA
Double Digestion of Insert DNA v1
Authors: Dusseldorf Igem
Published: October 2019

Combined enzyme volume should not exceed 1/10 of the total reaction volume. For double digestion with two FastDigest restriction enzymes, mix: Write down the name DNA tube used and its concentration. clean and concentrate the sample after digest in 10µL Water PCR Purified 2016.07.25ng/uLGene DNA Tube X50ComponentVolume x2µl]Sterile MilliQ Water2410x FastDigest Buffer4PCR-amplified DNA8FastDigest Enzyme 12FastDigest Enzyme 22Total Volume40Total ng of DNA400 Mix gently and spin down. Incubate at enzyme suitable conditions (45min) Inactivate the enzyme at suitable conditions
Bradford protein assay in 96-Well plate v1
Authors: Dusseldorf Igem
Published: October 2019

Assay for quantification of protein by comparing measured Absorbance at 595 nm to bovine serum albumine standard Bovine serum albumin (concentrated >200 µg/ml) Roti-Quant 5x (ROTH) 96 Well Plate Plate Reader Standard measurements Dilute your BSA stock solution to 200µg/ml in the same buffer used for your solution of interest. Dilute the Roti-Quant 5x reagent at a rate of 2:7,5. For 15 ml solution, this means 4 ml Roti-Quant added to 11 ml of Water. Create 200 µl each of standard concentrations according to the following table: Concentration [µg/ml]Volume of stock neededVolume of solution buffer needed002002020180404016060601408080120100100100 Work in Triplicates. Pipette 50µl of the standards into the 96-Well plate Add 200 µl of the diluted Bradford reagent to each well. Incubate for 5 minutes at room temperature Measure the OD595 for each well. Create a regression line from the averages of each concentrations' measurements Protein concentration measurements Dilute your solution of interest 1:20 or 1:40, depending on expected protein levels. Work in triplicates and use blanks. Pipette 50 µl of each dilution into a well on the 96-Well plate. When working with solutions containing pigments, prepare additional wells to which NO Bradford reagent will be added Add 200 µl of the diluted Bradford reagent to each well. For the pigment controls, add 200 µl of solution buffer instead. Optimally, use a multi-pipette to reduce the time needed for adding the reagent. Incubate for 5 minutes at room temperature Measure the OD595 for each well. When processing the data, correct the measurements for the blanks. When pigments are present in the solution, correct the OD595 by subtracting the OD595 of the pigment controls from the appropriate measurements. Determine the amount of protein by putting the achieved OD595 of your solution of interest into the regression formula and multiplying by the dilution factor.
Disruption of Synechocystis cells v1
Authors: Dusseldorf Igem
Published: October 2019

Protocol for disrupting Synechocystis cells to get soluble and non-soluble protein in different fractions Carry out all steps on ice Thylacoid-buffer (TP) 50 mM HEPES/NaOH 5 mM MgCl2 50 mM EDTA. pH 8 1 Tablet Protease inhibitor (Roche complete ULTRA tablets) per 10 ml TP Cell disruption Add 200 µl TP to a pellet of 20 ml Cell culture of OD750 ~0,5 and resuspend the pellet Add ca. 200 µl glas beads (1:1 mix of 0,1mm beads and 0,25 mm beads) Use program 2 of the precellys to disrupt the cells at room temperature, put on ice immediately afterwards Centrifuge for 5 min at 4°C and 4000 rpm to seperate glas beads and cellular waste from protein Take supernatant (Whole cell extract 1) Wash glas beads with 200 µl TP and repeat Precellys disruption Centrifuge for 5 min at 4°C and 4000 rpm to separate glas beads and cellular waste from protein Take supernatant (Whole cell extract 2) Mix Whole cell extract 1 and 2 Optional: Centrifuge for 45 min at 21000 rpm and 4°C to seperate soluble from non-soluble protein. Soluble protein will contain Phycocyanin, non-soluble protien will contain Chlorophyll. Freeze the protein until use, keep on ice when using it.
Stranded Transcript Count Table Generation from Long Reads v9
Authors: A Eccles David
Published: October 2019

This protocol is for comparing different samples at the transcript level, using long reads that are mapped to transcripts. Input(s): demultiplexed and oriented fastq files (see protocol Preparing Reads for Stranded Mapping), transcript reference fasta file, annotation file Output(s): transcript table, sorted by differential coverage, annotated with gene name / description / location
NucleoSpin® Gel and PCR Clean-up v1
Authors: Dusseldorf Igem
Published: October 2019

Buffer NTI NucleoSpin® Gel and PCR Clean-up Column NucleoSpin® Gel and PCR Clean-up Collection Tube (2ml) Buffer NT3 Buffer NE / nuclease-free water Solubilize gel slice For each 100 mg of agarose gel < 2 % add 200 μL Buffer NTI. For gels containing > 2 % agarose, double the volume of Buffer NTI. Incubate sample for 5–10 min at 50 °C. Vortex the sample briefly every 2–3 min until the gel slice is completely dissolved! Bind DNA Place a NucleoSpin® Gel and PCR Clean-up Column into a Collection Tube (2 mL) and load up to 700 μL sample. Centrifuge for 30 s at 11,000 x g. Discard flow-through and place the column back into the collection tube. Load remaining sample if necessary and repeat the centrifugation step. Wash silica membrane Add 700 μL Buffer NT3 to the NucleoSpin® Gel and PCR Clean-up Column. Centrifuge for 30 s at 11,000 x g. Discard flow-through and place the column back into the collection tube. Dry silica membrane Centrifuge for 1 min at 11,000 x g to remove Buffer NT3 completely. Make sure the spin column does not come in contact with the flow-through while removing it from the centrifuge and the collection tube. Note: Residual ethanol from Buffer NT3 might inhibit enzymatic reactions. Total removal of ethanol can be achieved by incubating the columns for 2–5 min at 70 °C prior to elution. Elute DNA Place the NucleoSpin® Gel and PCR Clean-up Column into a new 1.5 mL microcentrifuge tube (not provided). Add 15–30 μL Buffer NE and incubate at room temperature (18–25 °C) for 1 min. Centrifuge for 1 min at 11,000 x g.
Reverse transcription of RNA to cDNA v1
Authors: Dusseldorf Igem
Published: October 2019

100 ng RNA 40x yellow sample buffer random hexamer primers 5x RT-buffer dNTP Mix (10 mM of each nucleotide) RevertAid Reverse Transcriptase You will require 100 ng for RT and 100 ng for -RT control (include a -RT control for each sample!) Preparation of 1.33X yellow buffer 33,25 µL 40x yellow sample buffer + 966,75 µL H2O Start In PCR stripes, pipet in the following order: 100 ng template RNA 1 µL random hexamer primers RNase-free H2O to 12,5 µL volume Prepare a Mastermix of the following reagents: 4 µL 5x RT-buffer 0.5 µL RiboLock RNase-Inhibitor 2 µL dNTP Mix (10 mM of each nucleotide) 1 µL RevertAid Reverse Transcriptase Add 7.5 µL Mastermix to each reaction For your -RT control, pipet 100 ng RNA in PCR stripes, leave out buffer and everything, just add H2O to a final volume of 20 µL. Mark as -RT so you can distinguish it from your actual cDNA! PCR Programm 10 min 25 ˚C 60 min 42 ˚C 10 min 70 ˚C After completion of RT reaction: Add 60 µL 1,33 x yellow sample buffer to each reaction cDNA can be stored at 4 ˚C for a short time, otherwise, freeze at -20 ˚C
Growth curve analysis v1
Authors: Kuiper Sebastiaan
Published: October 2019

To observe the potential of defense mechanisms of either native or synthetic systems in Escherichia coli (and more) when incubated with a bacteriophage stock.
ONT Library Preparation v1
Authors: Reddington Kate , Eccles David , O’Grady Justin , M. Drown Devin , Hestbjerg Hansen Lars , Kjærgaard Nielsen Tue , Ducluzeau Anne-Lise , M. Leggett Richard , Heavens Darren , Peel Ned , P. Snutch Terrance , Bayega Anthony , Oikonomopoulos Spyros , Ragoussis Jiannis , Barry Thomas , van der Helm Eric , Jolic Dino , Richardson Hollian , Jansen Hans , R. Tyson John , Jain Miten , L. Brown Bonnie
Published: October 2019

Newly released Rapid Low Input by PCR Barcoding Sequencing Kit (SQK-RLB001); minor adjustments indicated by (*).
A Musa de Aristófanes: passarinho cantador
Authors: Barbosa Tereza Virgínia Ribeiro
Published: October 2019

Resumo: Este artigo trata das Musas, de comédia e de Aristófanes. A associação desses três temas, todavia, vai restringi-los a um só: a Musa da comédia a quem os gregos antigos chamavam Tália. A abordagem dessa divindade na análise será como uma voz, ou melhor, como o som do riso deseducado e irreverente provocado através da alegria, da correção e até mesmo do desejo de vingança.
Looking at Europe through a Basque lens: Ethnolinguistic considerations of two worldviews
Authors: Frank Roslyn May
Published: October 2019

W artykule stawia się tezę, iż lingwokultura baskijska daje wgląd w ramy pojęciowe odzwierciedlające dawny, animistyczny obraz świata, przywołujący kosmologie relacyjne, które – jak wiemy z danych etnograficznych – charakteryzowały społeczności zbieracko-łowieckie. W tym sensie, jeśli język baskijski określa się jako pre-indoeuropejski, powstaje pytanie, co to oznacza z punktu widzenia utrwalonej w nim kosmologii, zwłaszcza w kontekście wierzeń, obecnych wśród Basków jeszcze pod koniec XX w., jakoby ludzie pochodzili od niedźwiedzi. Dane etnograficzne i językowe wskazują na możliwość istnienia podobnego animistycznego językowokulturowego substratu na znacznym obszarze Europy w okresie, kiedy utrwalały się tam języki indoeuropjeskie i obecne w nich ramy pojęciowe. Wykorzystując metodologiczne i teoretyczne narzędzia lingwistyki kulturowej oraz pojęcie świata społecznego (świata życia, niem. Lebenswelt, ang. lifeworld) w ujęciu Jürgena Habermasa, definiowane jako przekazywany kulturowo i organizowany językowo zasób wzorców interpretacyjnych, poddano analizie trzy biegunowo ustrukturowane asymetrie, mocno zakorzenione w myśli zachodniej: mężczyzna/kobieta, człowiek/zwierzę i kultura/natura. Wszystkie opierają się na koncepcji wyjątkowości człowieka w relacji do innych bytów. Jednak kiedy rozważa się je w perspektywie ram pojęciowych zakodowanych w języku baskijskim, opozycje te znikają lub nabierają innego kształtu, zgodnie z ontologią animistyczną i związanym z nią pojęciem relacyjnej tożsamości indywidualnej. Innymi słowy, omawiane w artykule ramy pojęciowe wyrastające z lingwokultury baskijskiej często pokrywają się z takim rozumieniem animizmu, wedle którego wyraża on pewnego rodzaju ontologię relacyjną, podkreślającą i ściśle łączącą ze sobą pojęcia pokrewieństwa, wzajemnej pomocy i ogólnie wzajemności. Wyłaniający się z tych kontekstów obraz świata umożliwia niestandardowe spojrzenie na myśl zachodnią i rozwój pojęć w dawnej historii Europy.
Językowy obraz świata zdehumanizowanego: na przykładzie obrazu chorych umysłowo w powieści Elfriede Jelinek Die Klavierspielerin i jej przekładzie na język polski autorstwa Ryszarda Turczyna
Authors: Kubaszczyk Joanna Maria
Published: October 2019

Przedmiotem analizy jest fragment powieści Elfriede Jelinek Die Klavierspielerin oraz jej przekład na język polski dokonany przez Ryszarda Turczyna. Powieść Jelinek można uznać za powieść społeczną, w której autorka przeprowadza nie tyle analizę jednostkowego losu, ile analizę społeczeństwa, przedstawioną na przykładzie jednostki będącej „produktem” społecznym. Analiza kondycji człowieka i społeczeństwa odbywa się u Jelinek poprzez język, który bezlitośnie dezawuuje sposób myślenia bohaterów i mechanizmy społeczne. W artykule pokazane jest, w jaki sposób poprzez język Jelinek odsłania współczesną dehumanizację w odniesieniu do osób starszych i chorych psychicznie. Autorka w oparciu o teorię metafory kognitywnej analizuje tekstowy obraz świata, zakładając za Lakoffem i Johnsonem i pośrednio również za Jelinek, że metafory językowe można traktować jako manifestacje metafor myślowych. Jednocześnie stara się odpowiedzieć na pytanie, czy i na ile ten językowy obraz świata został odtworzony w przekładzie na język polski.
Внутренняя форма слова и ее реализация в древних славянских текстах
Authors: Кожинова Алла
Published: October 2019

W artykule dokonano analizy udziału wewnętrznej formy słowa w tworzeniu tekstu, a mianowicie zbadano kwestię, czy pamięć historyczna słowa wywiera wpływ na powstanie tekstu, łącząc jego poszczególne fragmenty. Rozpatrywana jest przezroczysta motywacja słowa, która bierze udział w tworzeniu konstrukcji zwanej figura etymologica, oraz motywacja deetymologizowana tworząca związki różnego rodzaju wewnątrz przestrzeni tekstowej. Badania przeprowadzono na bazie tekstów starosłowiańskich i cerkiewnosłowiańskich.
Память народно-культурной традиции в современном ритуальном дискурсе
Authors: Sedakova Irina Aleksandrovna
Published: October 2019

Pamięć jest jednym z konceptów najczęściej używanych we współczesnym dyskursie zarówno rosyjskim, jak i bułgarskim. Traktowana jest jako najwyższa wartość w wymiarze indywidualnym i zbiorowym, jako nieodłączna cecha humanistycznego, intelektualnego i duchowego rozwoju społeczeństwa. W artykule szczególną uwagę poświęcono badaniom folklorystycznym i etnograficznym oraz rozpatrzono podstawowe procesy, w których pamięć tradycji ludowej traktowana jest jako wartość społeczno-kulturowa. Na materiale rosyjskiej i bułgarskiej kultury szczegółowo przeanalizowano powody wariantywności pamięci i problem wybiórczości materiału faktograficznego podczas rewitalizacji. Na przykładzie obrzędów kalendarzowych i związanych z upamiętnieniem zmarłych zbadano podstawowe modele aktualizacji pamięci ludowej (modyfikacja starych i powstawanie nowych tradycji) oraz fakty związane z komercjalizacją pamięci (atrakcje turystyczne, show i widowiska).
Jak historia odkłada się w pamięci, jak pamięć odkłada się w języku
Authors: Chlebda Wojciech
Published: October 2019

 

Tematem artykułu jest zakreślenie ram pola badawczego tworzonego przez trzy tytułowe pojęcia: historia, pamięć, język. Ponieważ każde z nich jest wieloznaczne, a na dodatek w różnych sytuacjach odnoszone są do różnych porządków ontologicznych (do rzeczywistości pozajęzykowej i do rzeczywistości tekstowej, narracyjnej), autor stara się doprecyzować znaczenia odnośnych wyrazów i pokazać złożone relacje, jakie występują zarówno między poszczególnymi znaczeniami każdego z wyrazów oddzielnie (a więc pomiędzy „historią1” i „historią2” z jednej strony oraz między „pamięcią1” i „pamięcią2” – z drugiej), jak też, w układzie „horyzontalnym”, między „historią1” i „pamięcią1” oraz między „historią2” a „pamięcią2”. Autor uważa, że każdy z tych porządków rzeczy ma odrębną charakterystykę językową, istnieje jednak pięć cech, które między trzema konstruktami: „historią2” (tj. historiografią), „pamięcią2” (relacjonowaniem zawartości pamięci) i językowo-kulturowym obrazem świata stanowią wspólny mianownik; to podmiotowość, narracyjność, selektywność, interpretacyjność i ujęzykowienie. Ten wspólny mianownik pozwala na zestawianie i konfrontowanie z sobą zróżnicowanych obrazów tego samego wycinka przeszłości.
Lirik Olan Politiktir: 1980 Sonrası Türk Şiirinde Dişil Dilin Oluşumu
Authors: SİVRİ Tuğba
Published: October 2019

Hem dünyada hem Türkiye’de siyasal ve kültürel olarak bir kırılma noktasını imleyen1980’lerde Türk şiiri, askeri darbe sonrası oluşan baskı ortamında “içe dönmüş” ve “kişisel”olana yönelmiştir. Bu durum kimi eleştirmenlerce şiirin apolitizasyonu olarak yorumlansa da1980’ler, daha önceki siyaset biçimlerine benzemeyen, daha farklı politik akım ve oluşumlarasahne olmuştur. Türkiye’de yükselen radikal feminizm de bu farkı politik akımlardan biridir.Batı’da 1960’larda ortaya çıkan radikal feminizmin “kişisel olan politiktir” sloganı ve Fransızfeministlerin, kadınların eril dili kırarak kendi dil ve kültürlerini oluşturmalarının kadınözgürlüğü için şart olduğu argümanı, 1980 sonrası Türk edebiyatında ve kültürel üretimalanında karşılık bulmuştur. Bu çalışmada 1980 sonrası Türk şiirinin üç önemli kadın ismiNilgün Marmara, Birhan Keskin ve Didem Madak’ın şiirlerini, lirik şiirin barındırdığı politikpotansiyel ve dişil dilin inşası bağlamında analiz ettim. Bu üç şairin ortak yönlerineodaklanarak bir “dişil dil iskeleti” çıkarmaya çalıştım. Sonuç olarak bu üç şairin, “ev”i (yaniözel alanı) sorunsallaştırarak; Tanrı/baba/erkeğe isyan ederek; betonlaşma ve doğatahribatıyla yükselen kapitalist kültüre karşı doğaya dönüşü savunarak ve en önemlisi kadınbedenini, kadınların kendi ağızlarından, kendi “dil”leriyle yazarak dişil bir dil kurduklarınıgözlemledim. Ev içi deneyimlerin (evden kaçış, evi kurmak, evi düzeltmek de dâhil) ve kadınbedeninin (menopoz, adet görme, cinsellik vs.) şiire taşınması, ataerkil ideolojinin yok saydığıve üstünü örttüğü gerçeği gösterdiği ölçüde politiktir. Keskin, Madak ve Marmara, lirik şiirihem politik hem de dişil bir yerden kurmuşlardır.
ACTUAL QUESTIONS OF PERINATAL VIRAL HEPATITIS C PREVENTION
Authors: Galova Elena A.
Published: October 2019

Transplacental HCV-antibodies circulate in the blood of infants during the first year of the life and diagnosis of HCV-transmission is difficult. Aim: to study informativeness of serological diagnostic tests in anti/HCV-positive infants. Material and methods. the study was conducted in two groups of infants: RNA-positive (n=28) and RNA-negative (n=277). All children were born from a pregnant woman with chronic viral hepatitis C. The authors determined the sensitivity, specificity and accuracy of serological diagnostic tests for HCV transmission in infants: anti/HCV total, anti-HCcore IgG, anti-HCcore IgM, anti-HCNS3 IgG, anti-HCNS3 IgМ, anti-HCNS4 IgG, anti-HCNS4 IgМ, anti-HCNS5 IgG, anti-HCNS5 IgМ. Results. Detection of anti-HCV IgG-antibodies in the first 9 months of a child’s life has a high sensitivity but low specificity and low diagnostic efficacy; detection of anti HCV-IgM antibodies in the blood of the infant has significant specificity and high diagnostic efficacy. Discussion. The terms of examination of infants for viral hepatitis C are regulated by Sanitary Regulations and Standards (SanPiN 3.1.3112-13 Prevention of viral hepatitis C). We found that the detection of IgG antibodies in the blood of infants who were born to HCV-positive women has low diagnostic efficacy and will not lead to a correct diagnosis of perinatal HCV- transmission. It is necessary to develop and make changes in sanitary epidemiological rules. Conclusion. detection IgG-antibody is not informative during the first half of the infant’s life, but detection IgM-antibody is highly specific and accurate serological test for diagnostic HCV-transmission to child from mother with chronic viral hepatitis C.