Aug 17 2014

Partnership for Change Conference 2014

2014-05-15 16.22.56

On the day of May the 15th, I have joined the Partnership of Change 2014 conference representing ALIM Institution. I was invited to the conference as a social entrepreneur by the Kavli Trust, to whom I am grateful.

The conference was full of inspiring talks and discussions. I met brilliant people from around the world and shared interesting conversations about partnership, change, social entrepreneurship, development and impact investment. I have learnt about the term impact investment due to a mind opening session about this topic. From the conversations I made, the one with 2011 Nobel Peace Prize laureate Leymah Gbowee was the nicest. I had also the pleasure to listen to her talk and take a selfie with.

I should also mention that the location (Gamle Logen in Oslo) was great, the organization was flawless and lunch was very pleasant.

Feb 02 2014

Aşı ve İlaçlar

Note: This is a post to convince Turkish parents to not to trust anti-vaccine conspiracy theories.

Aşı karşıtı söylemlere maruz kalıyoruz. Özellikle ebeveynler çocuklarına aşı yaptırmakta tereddüt yaşayabiliyor. Şüpheci olmak çok önemli lakin şüphe ile komplo teorisini ayıran şey nedir? Doğruluğu kontrol edilemeyen/ispatlanamayan iddialara dayanan şüpheler komplo teorisidir. Bu yüzden iddiaları iyi değerlendirmek gerekir.

Aşı ya da herhangi bir ürün karşıtı kampanyalar hep üreticilerinin para kazanması üzerine kurguluyor argümanlarını. Peki nasıl olmalı? Teknolojik ya da tıbbi bir buluş, mucidine para getirmezse (patent sistemi olmazsa mesela) dünyada ilerleme nasıl sağlanacak, buluşlar nasıl yapılacak? Takdir edersiniz ki şu an baktığınız ekran, internet, altınızdaki araba, metro, uçak ve dahi aşılar, ilaçlar ve diğer tüm tıbbi yenilikler rekabet üzerine dayalı serbest piyasa ekonomisinin sonuçları. Başarılı olabilen farklı bir sistem görülmedi henüz dünyada. “Hiç mi suistimal yok” derseniz, haklısınız tabii ki var derim. Menfaatin olduğu her yerde (ki para en önemli menfaatlerden) mutlaka suistimal var. Suistimal edilmeyen hangi meslek var ki?

Peki kontrol mekanizması var mı? Elbette var. Örneğin kimse bahçesinden çıkan suyu şişeleyip satamaz Sağlık Bakanlığı’ndan izin almadan. Aynı şekilde basit bir el kremi bile Sağlık Bakanlığı’ndan izin almadan piyasaya sürülemez. İlk izinden sonra kontroller de devam eder. Bakanlığın ifşa ettiği sahte balları, kusurlu suları vs hatırlayınız.

Aşılarda ve ilaçlarda bu durum çok daha ciddidir. İlaçlar piyasaya sürülmek için ABD’de meşhur Food and Drug Administration’dan (FDA) 4 aşamada izin almaya tabidirler. Prosedür FDA tarafından iki sayfada şurada İngilizce özetlenmiş. FDA’nın yanında ülkelerin sağlık bakanlıkları ve benzer organlar da var.

FDA iznini almaya çalışan ilaçlardan %95’i testleri geçemiyor (kaynak), bu çok ciddi bir oran. Yine aynı makaleye göre ArGe harcamaları ve regülasyonları geçmek için harcanan miktarlar ilaç başına 350 milyon ile 5 milyar dolar arasında değişiyor. Sanırım bu sayılar neden ilaçların ve aşıların satılması ve üreticilerinin bundan kar etmesi gerektiği konusunda şüphe bırakmıyor.

Peki sistemde hata olmuyor mu? Elbette oluyor ve sonradan o ilaç/aşı piyasadan çekiliyor. Örneğin FDA’nın başlattığı Vaccine Adverse Event Reporting System (Aşı yan etkileri şikayet sistemi) ile aşı şikayetleri iletiliyor sisteme 1990’dan beri. Lakin o oldukça düşük hata oranlarına bakarak tüm sektörü kötülemek insafsızca olur kanaatindeyim. O düşük hata oranları yüzünden tüm ilaçları reddetmek, çok faydalı ve hayat kurtaran ilaç ve aşıların faydalarından mahrum kalmak demek. Bunu aşağıda çiçek aşısı ile örnekledim. Aynı şekilde modern araçlar insan ölümüne sebep oluyor diyerek taşıtları reddetmiyoruz mesela.

Aşıların faydalarını UNICEF raporundan okuyalım:

Aşılanma olmasaydı görülecek yıllık ölüm Engellenen Görülen % Engellenen
Çiçek hastalığı
5.0 milyon 5.0 milyon 100
Difteri
260,000 223,000 37,000 86
Boğmaca 990,000 630,000 360,000 64
Kızamık 2.7 milyon 1.6 milyon 1.1 milyon 60
Neonatal tetanoz 1.2 milyon 0.7 milyon 0.5 milyon 58
Hepatit B 1.2 milyon 0.4 milyon 0.8 milyon 33
Tüberküloz 3.2 milyon 0.2 milyon 3.0 milyon 6
Kalıcı çocuk felci 640,000 550,000 90,000 86
Sıtma ve diğer parazitik enfeksiyonlar 2.2 milyon 2.2 milyon 0
HIV/cinsel yolla bulaşan hastalıklar 1.3 milyon 1.3 milyon 0
İshal/tifo 3.0 milyon 3.0 milyon 0
Üst solunum yolları enfeksiyonu
3.7 milyon 3.7 milyon 0

Mesela çiçek hastalığı (smallpox) dünyadan tamamen kaldırılmış aşılar sayesinde. Yılda 5 milyon insanın hayatının kurtulduğu hesaplanıyor. Peki ya yan etkiler? Çiçek aşısı yüzünden her 1 milyon kişide 1-2 ölüm gerçekleşmiş bugüne kadar (kaynak).Yılda 5-10 çocuk ölüyor, bir kısmı da hayati olmayan bazı sorunlar yaşıyor ama 5 milyonu kurtuluyor. Kar zarar hesabı ortada değil mi?

İşte aşı karşıtı kampanyalar bu büyük resmi görmek yerine minimum düzeyde olan yan etkileri servis ediyor maalesef.
Batı ülkelerinde diğer birçok hastalık da görülmüyor artık aşılar sayesinde yine (çocuk felci gibi). Maalesef dünyanın diğer taraflarında bu hastalıklar hala var, bunun en önemli nedenlerinden birisi de aşı karşıtı kampanyalar. Eğer komplo teorilerine inansaydım, aşı karşıtı kampanyaların “dış mihrakların” gelişmemiş ülkeler üzerine oynadığı oyunlardan birisi olduğunu söylerdim.

Diğer bir veri: 1995’de Hepatit A aşısı ilk kez piyasaya sürüldü. O günden bu yana Hepatit A vakalarında %89 azalma görüldü. Aynı kaynaktan: 1998’de ABD’de piyasaya sürülen rotavirus aşısı bir yıl sonra yan etkileri yüzünden geri çekilmiş. Aynı şekilde 1999’dan itibaren FDA, civanın (ağır bir metal) tüm ürünlerden, ilaçlardan ve aşılardan çıkartılmasını şart koşmuş. Demek ki sistemin sigortaları işliyor.

Şu grafiklere de göz atarsak bence ilaçlar ve aşıların insan yaşamı üzerine etkisi zihinlerde açığa kavuşacaktır:

1) Ülkelerin ortalama yaşam süreleri (kaynak):

Life_Expectancy_2005-2010_UN_WPP_2006
Gelişmişlikle ne kadar doğru orantılı değil mi? Batı ülkelerinde ortalama yaşam 80’e ulaşmış, Türkiye hala 70-72 kuşağında. Afrika’nın hali içler acısı. Bu oranları etkileyen başka faktörler (savaş gibi) de olduğunun farkındayım, lakin modern tıbbın ana etken olduğunu düşünüyorum.

2) Modern tıbbın etkisi: ABD’de yıllara göre ortalama yaşam süresi (kaynak)

yasam
55 yılda ortalama yaşam süresi (life expectancy) 68’den 78’e cıkmış ABD’de. Yani “yeni icatlar” insanları öldürmüyor, bilakis hayatı uzatıyor. Diğer bir kaynak.
3) Doğan her 1000 çocuktan kaçı 1 yaşına gelmeden ölüyor? (kaynak ve resim)

Infant_mortality_rate_world_map

Yine dünyanın bölgelerini kıyaslamak bizi önemli sonuçlara ulaştıracaktır.

4) Çocuk ölüm oranları (infant mortality rate) dünya genelinde düşüyor (kaynak). World: dünya, More developed regions: gelişmiş bölgeler, Latin America and the Caribbean: orta-güney Amerika ve Karayipler
Infant_Mortality_Rate_by_Region_1950-2050
Tüm dünyada 1950’de her 1000 doğumdan 150’sı, şimdi ise 45’i bir yaşına gelmeden ölüyor.

Sisteme güvenmek ya da güvenmemek sizin elinizde tabii ki. Güvenmemek yalnızca ilaç şirketlerinin değil, FDA, Dünya Sağlık Örgütü (WHO), UNICEF ve TC Sağlık Bakanlığı gibi birçok kurumun da bu komplonun bir parçası olduğunu iddia etmekle mümkün oluyor. Hatta aşı karşıtı iddialarda da geçtiği gibi etrafımızdaki tüm doktorları “sorgulamayan kör inançlı”, “komploya boyun eğmiş”, “kişisel çıkarı için insanların sağlığını hiçe sayan” olarak nitelememiz gerekiyor.

Son olarak aşılar ilaç şirketlerinin karını arttırmak yerine düşürüyor. Biliyorsunuz ki birçok ülkede çocuk aşıları ücretsiz yapılıyor. Hükümetler, bütün çocukların aşılanmasının masrafının, aşılanmazsa hastalanacak çocukların bakım masraflarından çok daha az olacağını bildiği için bu yükün altına giriyor. Yani yaşanacak can kayıplarını ve hastalıklardan dolayı kaybedilecek zaman ve iş gücünü bir kenara bıraksak dahi, hastalıkların maddi külfeti (yani ilaç şirketlerine kazandıracağı para) aşıların kazandırdığından çok daha fazla olacak.

Ek okuma: Aşı karşıtı kampanya nasıl başladı ve yakın zamanda hangi aşıyla önlenebilecek salgınlar görüldü dünyada (Ingilizce)

Sep 30 2013

Guided my colleagues in Istanbul

We had a 3 full day tour in Istanbul with my colleagues as a team building event last August. Weather was fantastic; quite warm but not too hot. Have seen the main attractions and tasted great food!

 

Jul 23 2013

Turkish Scientists Abroad 2013 Assembly

YTBIK 2013

End of the meeting

 

I was invited by TUBITAK to Turkish Scientists Abroad 2013 Assembly (Yurt Dışındaki Türk Bilim İnsanları 2. Kurultayı) on 4-5 July. There were about 100 brilliant scientists, the majority of which were from academia, working in highly respected institutions. There were also R&D scientists from some companies, but less in number. Finally, there were professors and rectors from Turkish institutions, representatives of Turkish companies and members of TUBITAK. It was an amazing opportunity to be introduced to such people, especially in a relaxed environment.

invited by TUBITAK to Turkish Scientists Abroad 2013 Assembly (Yurt Dışındaki Türk Bilim İnsanları 2. Kurultayı) on 4-5 July. There were about 100 brilliant scientists from abroad, the majority of which work in highly respected academic institutions. There were also R&D scientists from large companies, but less in number. Finally, there were professors and rectors from Turkish institutions, representatives of Turkish companies and members of TUBITAK. It was an amazing opportunity to be introduced to such people, especially in a relaxed environment.

The meeting was designed to discuss 4 priority topics that TUBITAK wants to improve in Turkey: education, health care technologies, technology transfer (from academia to industry) and energy. I was in the education section perhaps because of a mistake. Though I did not mind as the minister of education joined the first session. In the presence of the minister Nabi Avci, I brought up the problems some Turkish PhD students including myself face with the compulsory military service. I also tried to draw attention to some problems in higher education system from a (relatively) fresh graduates’ viewpoint during other sessions.

The meeting was formally closed by a half an hour speech by the prime minister Erdogan. He briefly thanked the attendees and asked to “pay back” to the motherland. Then he spent most of his time about the coup staged in Egypt, giving examples from the Turkish democracy experience under military coups.

The cherry on the top was the Bosphorus boat tour at night with great food, Turkish music and dance.

Talha Gokmen ytbik 2013

Dec 12 2012

Under pressure

explosiveScientists are well aware of the fact that pressure can change the outcome of a reaction to yield products that are ?impossible? to obtain otherwise. Pressure can also alter the behavior of matter. Gas molecules behave like liquid under high pressure and totally different characteristics emerge when supercritical conditions are reached. Another well known fact is that pressure can change the behavior of scientists and make them produce ?impossible? data. Being under a high pressure to publish is a result of current publication-based rewarding system of the academic world.[1] Academic rewards include reputation, grants and promotions (fame and money in other words, the two that top the list of human weaknesses) which are often received due to number of publications [2] instead of quality of research. Fabrication, falsification, plagiarism and concealing ?unexpected? results comes to life [3] when scientist (often deliberately) neglects the conscience for the sake of publishing more.

Believing that fraudsters will eventually come to surface is too naive to my own experience. Fraud unveils mostly in the cases where the driving force for such scientific misconduct is fame and a breakthrough is fabricated to publish in a distinguished journal such as Nature and Science. The fact that the number of retracted papers from a lower impact factor journal is 9 times less compared to that of Science [4] should certainly not mean that there are less articles need to be retracted from lower impact factor journals. I would rather discuss that there are much more articles to be retracted in lower impact factor journals but retraction happens much less in that case. The reason is that researchers certainly do not have the necessary time to follow all the related literature due to ever-increasing number of publications, that in turn a result of the pressure to publish. 

This vicious circle is one of the major challenges in scientific publishing and needs to be addressed immediately by academic consensus to my opinion. If you are not aiming for the biggest fish, you can rather easily publish in one of the numerous lower impact factor journals to reach your academic reward. Experience of many graduate students on not being able to reproduce results (generally partially) even from well respected journals encourages me to draw this conclusion. You may lose months of your precious time if you are trying to apply results of a fabricated publication to your own research. It makes you surer of yourself when you do not receive a reply from the corresponding author to your questions, which is often the case to my regret.

Another well known but unspoken way of artificial CV improving is the practice of adding names of those ?scientists in need? (postdocs or senior graduate students) to a paper of another researcher (often junior graduate student) although they have no contribution to the research of ?victim? in any means. It is generally the merciful promoter who decides which names to include to an article that may increase one by one during the pre-submission correction rounds. Junior graduate student would not dare to contest this mercy due to several reasons, the most important being the hierarchy. Since most of the academic rewarding systems, such as grant approval, counts the number of publications where place of your name in the highly populated author line-up does not really matter, ?scientist in need? may become highly successful. One solution to my opinion can be the obliged declaration of author contributions for submitted articles, which is rarely practiced at the moment. Another way to cope this misconduct can be obliged anonymous individual recognition of contribution from every other author which can be easily done via internet.

stressedFinally, perhaps the most ?innocent? and commonly practiced artificial CV improvement method is dividing the results as much as possible to publish more than one article. To my belief all this misbehavior can be at least partially avoided by a general intention of removing the pressure on academia and changing the basis of scientific rewarding. Research can be most of the times seriously frustrating for a graduate student. Every graduate student or postdoc wants to prove him/herself and is very ambitious at the start due to ?promising? projects, often highly overrated by promoter. Working day and night, sacrificing the weekends may not be enough to ever see these promised results just because they do not exist. At this point, it is difficult to carry on for you as a young researcher and convince yourself that failure is not your fault. Then there can be several conditions (supercritical conditions) that may drive the young researcher to falsify the data: A highly demanding promoter, fear of disapproval for the next contract extension for which success is sometimes determined as a prerequisite by the promoter, fear of being ignored among ?successful? colleagues, just finishing the current degree with no more troubles and move further on. Professional support from the promoter should be the key for avoiding the young researcher to do such mistakes.

M. Talha Gokmen

Originally written on 06 July 2010 while still a grad student

References

[1] Jones, N., Nat Med 15 (10), 1101 (2009).

[2] Qiu, J., Nature 463, 142 (2010).

[3] Martinson, B. C., Anderson, M. S., and de Vries, R., Nature 435 (7043), 737 (2005).

[4] Cokol, M., Iossifov, I., Rodriguez-Esteban, R. et al., EMBO Rep. 8 (5), 422 (2007).

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Nov 11 2012

Chemically orthogonal trifunctional Janus beads

 

We have a new paper accepted by Chemical Communications. This becomes my 8th paper, 2nd in Chem Comm.

Chemically orthogonal trifunctional Janus beads by photochemical ?sandwich? microcontact printing

Tobias Kaufmann, Christian Wendeln, M. Talha Gokmen, Stefan Rinnen, Maria Becker, Heinrich F. Arlinghaus, Filip Du Prez* and Bart Jan Ravoo*

 

The novelty of this work, compared to the 2 earlier papers we published together with the Ravoo group, is that we introduce here reactive patches on beads that can be orthogonally functionalized in one pot reactions.

Download pdf version here

May 19 2012

Received BPRI annual PhD award in polymer science & technology

Beginning of May 2012, I have visited Belgium. It was a nice opportunity to see my ex-supervisor Filip Du Prez, ex-colleagues and friends, some of whom are also finishing their PhD soon. I actually realized that I may not find that many friends next time I visit Belgium.

I was actually invited to Belgian Polymer Group‘s 2012 Annual Meeting. The Belgian Polymer and Rubber Institute (BPRI) has chosen my PhD thesis for their Annual PhD Award in Polymer Science & Technology “for the best PhD work with a potential industrial valorization on a subject dealing with Polymer Science and/or Technology”. There was a small ceremony followed by a 15 min talk by me on my thesis. I also received very nice feedback on my talk from several people

I would like to express my gratitude to BPRI for offering this award and the supervisor of my PhD, Prof Filip Du Prez, for his support on my candidacy.

 

Mar 12 2012

How to write a scientific paper

Edited on 12 July 2012

I have been asked by many of my friends and colleagues about converting their research into text, how to write a scientific article in other words. I share my own experience here, hoping that it will be useful for some.

Writing a nice paper is not an easy job, especially if you are not a native English speaker (see this article if you are a non-native English speaker). It is even more difficult to write the first ever article of yours. Some students witness paper writing process when they are on undergraduate or master level. This is certainly good when the time comes for them to write their own paper. But not everyone, including myself, is lucky to have an article before their doctorate.

We scientists have to learn it like the way we developed many skills such as doing research. At the end, who else is capable of learning it if we are not? Don’t refrain from it, learn it as soon as you can. You will see that the procedure will teach you how to be consistent and convincing.

The golden rule: Read a lot of high quality articles (published in top journals), especially from prominent scientists. That certainly improves your scientific English. I was following more than 20 journals when I was doing my PhD. I (at least partially) read hundreds of papers so far. One professor told me once that he asks his students to read at least one article per week. So read one article per week (minimum) and “skim” the others. Skimming is going through the figures and their captions, also reading the abstract and conclusions.

There are many courses offered these days on ?scientific writing skills?, check if your institution offers one. There are also many books about it. It will be worthwhile to invest your time on these.

Writing a scientific article step-by-step:

Step 1      Literature Search: Do another complete literature search. Take your time for this. You should have done this several times throughout your work actually, especially in the beginning. Do not blindly trust on others, such as your promoter or supervisor. May be this was done before and your promoter missed it.
After doing the literature study, carefully read the most relevant papers to your work. While reading, highlight bullet points, take notes, do more literature search etc. In this stage, if well concentrated, your mind will prepare a plan for writing your own paper. When you answer (at least some of) these questions: why my research is important, what is the novelty of my research, to which questions does it answer, why is it better than the works of others, where does it fit into the existing field etc. Answering these questions will certainly help you build your plan: on which argument(s) you establish your paper, what you will talk about in the introduction, which figures you will add, how will you discuss your results and how you will conclude. The plan is actually your plan of selling your paper to the readers but also to the editor of the journal you are submitting and the reviewers.

 

Step 2      Figures: Now prepare all the figures (graphs, tables etc). You don?t need to prepare perfect versions in the beginning, just prepare easy versions. You can perfect them at the end.

You can use PowerPoint to prepare your figures. If that does not satisfy you, ask your experienced colleagues.

 

Step 3      Article type: Decide if you are going for a full article or a communication (the latter is generally harder, more restrictions apply and work should be really novel)

 

Step 4      Designate paragraphs: Literature search done, notes taken, figures are ready; now you can build up the structure of your paper. Lets say it is a full paper: Introduction, Results and Discussions, Conclusion will be three major sections. For each section, designate paragraphs by entering some phrases or keywords for each paragraph. This is very important in my point of view. For readability and clarity, each paragraph should have an aim and should give the reader one or two messages. So by deciding on the messages of each paragraph beforehand, you will ensure that your text will be consistent, free of repetitions and the readers will enjoy it.

For instance, you write a paper on a new cancer therapy based on multiple emulsions.

Introduction:

1st paragraph: Cancer

2nd paragraph: Cancer treatments in clinic

3rd paragraph: Other proposed cancer treatments in literature

4th paragraph: Define multiple emulsions and explain their use in treating diseases, especially cancer

5th paragraph: Talk about your work; why it is different than others, what is novel, what you did etc

Results & Discussions

This depends on your work of course. Figures will help you a lot to construct this part. You may start with some introducing sentences but don?t repeat the introduction section. You can also divide this section into sub-sections.

X-type emulsion: We prepared this and that. We found this and that. See Fig 1. It useful in this sense but it failed in XXX test

Y-type emulsion: We designed this emulsion. It is better.

Z-type emulsion: This is even better. Works for this and that.

Clinical trials

We found this and that. It showed us that y is useful for this. This  is because of xxxxx theory. Smith et al also found the same?

Now you are ready to start writing! Congratulations, you already made the hardest part.

 

Step 5      Actual writing: It is hard to start typing. You may spend hours in front of your computer without ending up in three sentences. Just concentrate and try, it will come. Do not give up!

I start with writing the introduction, others may start with results and discussion part. You already designated the paragraphs. Now fill the paragraphs with your sentences.

The platinum rule: Keep the language simple, avoid long and difficult to understand sentences. The shorter the article the better to read. Don’t you prefer to read 2-3 page communications over 10 page articles? Avoid repetitions and unnecessary words/sentences.

The silver rule: Do not plagiarize, meaning that do not take others sentences (or even your own sentences that are published elsewhere). See the definition of plagiarism in Wikipedia

 

Step 6      Write your conclusions: Read several conclusion sections of other articles if you need to. Point out the novelty of your work and briefly talk about your main findings. Be brave to praise your work but do not overdo it: do not claim that you found the ultimate solution to cancer :)

 

Step 7      Write an abstract: Here you will ask yourself the difference between the conclusion section and the abstract.  In abstract, you generally do not talk about your full results. Few sentences about the problem and your proposal to solve this problem.

For instance: Colorectal cancer is the most common cancer. Current treatments may have very bad side effects on patients. Here we present a new treatment method based on multiple emulsions. We prepare drug x as an emulsion and measure its lifetime in the body…

 

Step 8      Find a title: Most of the times, people read only titles. If a title is interesting, they go further into abstract and into main text. So try to find an “eye-catching title” as Prof Filip Du Prez used to tell me. He also told me that a title should not be too long. So try to find a balance. You can prepare 3 options and let your supervisor decide on the title.

 

Step 9      Find keywords

That is it! You are almost done. You should be happy by then. As you imagine, you will be much more happier once your paper is accepted for publication.

 

Step 10    Submission: This is a whole other process and I think it deserves a separate post. I guess your promoter will help you in this process if it is your first article. You should decide about the journal that you want to send your paper, learn the rules of this journal, download the template, decide about the referees that you will propose and write a good cover letter to the editor. I will try to explain this procedure and perhaps what follows next (when comments of referees return) in a separate post.

 

Good luck! Yeah, it is little bit of luck also.

M. Talha Gokmen

Note: George Whitesides is one of the greatest living chemists on earth, may be the greatest! You should read his suggestions as well.

Feb 19 2012

Latest paper is online

The second fruit of our collaboration with the group of Prof Ravoo is available online now: Bifunctional Janus Beads Made by ?Sandwich? Microcontact Printing and Click Chemistry

You can download the article from RSC website if you have a subscription. I also added a copyright-free pdf version of the article on the Publications page.

Feb 17 2012

ACS thanks authors and referees!

ACS has released this video just few days ago. I cannot help but ask myself if they are afraid of a similar reaction as the one against Elsevier (please read the previous post).

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