Mining Software Repositories for Release Engineers - Empirical Studies on Integration and Infrastructures-as-Code

RÉSUMÉ Release engineering (Releng) est le processus de la mise en production logicielle des contributions des développeurs en un produit intégré livré aux utilisateurs. Ce processus consiste des phases d’intégration, de construction et des tests, de déploiement et de livraison, pour finalement entrer au marché. Alors que, traditionnellement, la mise en production prend plusieurs mois pour livrer un produit logiciel complet aux clients, la mise en production moderne vise à apporter de la valeur au client plus rapidement, dans l’ordre des jours ou des semaines, pour recevoir de rétroaction utile plus rapidement et pour minimiser le temps perdu sur des fonctionnalités échouées. De nos jours, une panoplie d’outils et de techniques a émergé pour soutenir la mise en production. Ils visent essentiellement à automatiser les phases dans le pipeline de la mise en production, ce qui réduit le travail manuel et rend le processus reproductible et rapide. Par exemple, Puppet est l’un des outils les plus populaires pour Infrastructure-as-Code (IaC), ce qui automatise le processus de mettre en place une nouvelle infrastructure (par exemple, une machine virtuelle ou un conteneur dans lequel une application peut être compilée, testée et déployée) selon des spécifications textuelles. IaC a évolué rapidement en raison de la croissance de l’infonuagique. Cependant, de nombreux problèmes existent encore pour la mise en production. Par exemple, alors que de nombreux outils de la mise en production gagnent en popularité, le choix de la technique la plus appropriée exige des praticiens d’évaluer empiriquement la performance des techniques dans un contexte réaliste, avec des données représentatives. Pire encore, à un niveau plus haut, les ingénieurs de la mise en production doivent analyser le progrès de l’organisation dans chaque phase de la mise en production, afin de savoir si la prochaine date de sortie peut être respectée ou si des obstacles se produisent. De nouveau, il n’y a pas de méthode cohérente et établie pour ce faire. Pour aider les praticiens à mieux analyser leur processus de la mise en production, nous explorons la façon selon laquelle la fouille de référentiels logiciels (Mining Software Repositories; MSR) est capable d’analyser le progrès d’une phase de la mise en production ou d’évaluer la performance d’un outil de mise en production. MSR agit sur les données stockées dans des référentiels de logiciels tels que les systèmes de gestion de versions, les référentiels de bogues ou des environnements de révision technique. Au lieu que les développeurs, les testeurs et les examinateurs utilisent ces référentiels juste pour enregistrer des données de développement (telles que les changements de code, rapports de bogues ou des révisions techniques), MSR rend ces données actionnables en les analysant. Par exemple, en faisant l’extraction de l’information des changements de code source et de rapports de bogues, on peut recréer l’ensemble du processus de développement d’un projet ou de la mise en production. De nos jours, de nombreux référentiels logiciels à source libre sont disponibles au public, offrant des possibilités pour l’analyse empirique de la mise en production en utilisant des technologies MSR. Dans cette thèse, on a fait des analyses MSR pour deux phases critiques de la mise en production, c.-à-d. l’intégration et le provisionnement de l’environnement d’un logiciel (avec IaC), sur plusieurs projets larges à source libre. Cette série d’études empiriques ciblait de comprendre le progrès du processus de la mise en production et d’évaluer la performance des outils de point. Nous nous sommes concentrés principalement sur ces deux phases parce qu’elles sont essentielles dans la mise en production, et un grand nombre de données est disponible pour elles. D’abord, nous avons constaté que la révision technique et l’intégration de changements de code sont impactées par de différents facteurs. Nos résultats suggèrent que les développeurs réussissent à faire passer leurs contributions à travers la révision technique plus rapidement en changeant moins de sous-systèmes à la fois et de diviser une grande contribution en plusieurs contributions plus petites. En outre, les développeurs peuvent faire accepter leurs contributions plus facilement et plus rapidement en participant davantage dans la communauté de développeurs à source libre et d’acquérir plus d’expérience dans des sous-systèmes similaires. Dans cette étude sur le noyau Linux, nous avons trouvé que l’un des défis majeurs de MSR dans le contexte de la mise en production logicielle est de relier les différents référentiels nécessaires. Par exemple, le noyau Linux ou le projet Apache HTTPD utilisent tous les deux des listes de diffusion pour effectuer le processus de révision technique. Les experts examinent des contributions par courriel, et un fil de courriels est utilisé pour ramasser toutes les différentes versions d’une contribution. Cependant, souvent un nouveau fil de discussion, avec sujet différent, est utilisé pour soumettre une nouvelle révision, ce qui signifie qu’aucun lien physique étroit n’existe entre toutes les révisions d’une contribution. En plus, les versions révisées d’une contribution non plus n’ont de lien physique avec la version acceptée dans le référentiel de gestion de versions, à moins qu’un identifiant de validation soit affiché dans un courriel. Surtout quand une contribution a été révisée plusieurs fois et a beaucoup évolué en comparaison avec la version initiale, le suivi à partir de sa toute première version est difficile à faire. Nous avons proposé trois approches de différente granularité et de rigueur différente, dans le but de récupérer les liens physiques entre les révisions de contributions dans le même fil de courriels. Dans notre étude, nous avons constaté que la technique au niveau des lignes individuelles fonctionne le mieux pour lier des contributions entre différents fils de courriels, tandis qu’une combinaison de cette approche avec celle à base de sommes de contrôle réalise la meilleure performance pour relier les contributions dans un fil de courriels avec la version finale dans le référentiel de gestion de versions. Être capable de reconstituer l’historique complet de contributions nous a permis d’analyser le progrès de la phase de révision du noyau Linux. Nous avons constaté que 25% des contributions acceptées prennent plus de quatre semaines pour leur révision technique. Deuxièmement, pour évaluer la capacité de MSR pour analyser la performance des outils de mise en production, nous avons évalué dans un projet commercial une approche d’intégration hybride qui combine les techniques de branchement et de “feature toggles”. Des branches permettent aux développeurs de travailler sur différentes fonctionnalités d’un système en parallèle, en isolation (sans impacter d’autres équipes), tandis qu’un feature toggle permet aux développeurs de travailler dans une branche sur différentes tâches en cachant des fonctionnalités sous développement avec des conditions “if” dans le code source. Au lieu de réviser leur processus d’intégration entièrement pour abandonner les branches et de passer aux feature toggles, l’approche hybride est un compromis qui tente de minimiser les risques des branches tout en profitant des avantages des feature toggles. Nous avons comparé la performance avant et après l’adoption de l’approche hybride, et avons constaté que cette structure hybride peut réduire l’effort d’intégration et améliorer la productivité. Par conséquent, l’approche hybride semble une pratique valable. Dans la phase de provisionnement, nous nous sommes concentrés sur l’évaluation de l’utilisation et de l’effort requis pour des outils populaires de “Infrastructure-as-Code” (IaC), qui permettent de spécifier les requis d’environnement dans un format textuel. Nous avons étudié empiriquement les outils IaC dans OpenStack et MediaWiki, deux projets énormément larges qui ont adopté deux des langues IaC actuellement les plus populaires: Puppet et Chef. Tout d’abord, nous avons comparé l’effort de maintenance lié à IaC avec celui du codage et des tests. Nous avons constaté que le code IaC prend une partie importante du système dans les deux projets et change fréquemment, avec de grands changements de code. Les changements de code IaC sont étroitement couplés avec les changements de code source, ce qui implique que les changements de code source ou des tests nécessitent des changements complémentaires au code source IaC, et pourrait causer un effort plus large de maintenance et de gestion de complexité. Cependant, nous avons également observé un couplage léger avec des cas de test IaC et les données de provisionnement, qui sont de nouveaux types d’artéfacts dans le domaine de IaC. Par conséquent, IaC peut nécessiter plus d’effort que les ingénieurs expectent. D’autres études empiriques devraient être envisagées. L’ingénierie de la mise en production moderne a développé rapidement, tandis que de nombreux nouvelles techniques et outils ont émergé pour le soutenir de différentes perspectives. Cependant, le manque de techniques pour comprendre le progrès des phases de la mise en production ou d’évaluer la performance d’outils de la mise en production rend le travail difficile pour les praticiens qui ont à maintenir la qualité de leur processus de mise en production. Dans cette thèse, nous avons mené une série d’études empiriques en utilisant des techniques de fouille des référentiels logiciels sur des données de larges projets à source libre, qui montrent que, malgré des défis, la technologie MSR peut aider les ingénieurs de la mise en production à mieux comprendre leur progrès et à évaluer le coût des outils et des activités de la mise en production. Nous sommes heureux de voir que notre travail a inspiré d’autres chercheurs pour analyser davantage le processus d’intégration, ainsi que la qualité du code IaC.---------- ABSTRACT Release engineering (Releng) is the process of delivering integrated work from developers as a complete product to end users. This process comprises the phases of Integration, Building and Testing, Deployment and Release to finally reach the market. While traditional software engineering takes several months to deliver a complete software product to customers, modern Release engineering aims to bring value to customer more quickly, receive useful feedback faster, and reduce time wasted on unsuccessful features in development process. A wealth of tools/techniques emerged to support Release engineering. They basically aim to automate phases in the Release engineering pipeline, reducing the manual labor, and making the procedure repeatable and fast. For example, Puppet is one of the most popular Infrastructure-as-Code (IaC) tools, which automates the process of setting up a new infrastructure (e.g., a virtual machine or a container in which an application can be compiled, tested and deployed) according to specifications. Infrastructure-as-Code has evolved rapidly due to the growth of cloud computing. However, many problems also come along. For example, while many Release engineering tools gain popularity, choosing the most suitable technique requires practitioners to empirically evaluate the performance of the technique in a realistic setting, with data mimicking their own setup. Even worse, at a higher level, release engineers need to understand the progress of each release engineering phase, in order to know whether the next release deadline can be met or where bottlenecks occur. Again, they have no clear methodology to do this. To help practitioners analyze their Release engineering process better, we explore the way of mining software repositories (MSR) on two critical phases of Releng of large open-source projects. Software repositories like version control systems, bug repositories or code reviewing environments, are used on a daily basis by developers, testers and reviewers to record information about the development process, such as code changes, bug reports or code reviews. By analyzing the data, one can recreate the process of how software is built and analyze how each phase of Releng applies in this project. Many repositories of open-source software projects are available publicly, which offers opportunities for empirical research of Release engineering. Therefore, we conduct a series of empirical studies of mining software repositories of popular open-source software projects, to understand the progress of Release engineering and evaluate the performance of state-of-the-art tools. We mainly focus on two phases: Integration and Provisioning (Infrastructure-as-Code), because these two phases are most critical in Release engineering and ample quantity data is available. In our empirical study of the Integration process, we evaluate how well MSR techniques based on version control and review data explain the major factors impacting the probability and time taken for a patch to be successfully integrated into an upcoming release. We selected the Linux kernel, one of the most popular OSS projects having a long history and a strict integration hierarchy, as our case study. We collected data from reviewing and integration tools of the Linux kernel (mailing lists and Git respectively), and extracted characteristics covering six dimensions. Then, we built models with acceptance/time as output and analyzed which characteristics have impact on the reviewing and integration processes. We found that reviewing and integration are impacted by different factors. Our findings suggest that developers manage to get their patch go through review phase faster by changing less subsystems at a time and splitting a large patch into multiple smaller patches. Also, developers can make patches accepted more easily and sooner by participating more in the community and gaining more experience in similar patches. In this study on the Linux kernel, we found that one major challenge of MSR is to link different repositories. For example, the Linux kernel and Apache project both use mailing lists to perform the reviewing process. Contributors submit and maintainers review patches all by emails, where usually an email thread is used to collect all different versions of a patch. However, often a new email thread, with different subject, is being used to submit a new patch revision, which means that no strong physical links between all patch revisions exist. On top of that, the accepted patch also does not have a physical link to the resulting commit in the version control system, unless a commit identifier is posted in an email. Especially when a patch has been revised multiple times and evolved a lot from the original version, tracking its very first version is difficult. We proposed three approaches of different granularity and strictness, aiming to recover the physical links between emails in the same thread. In the study, we found that a line-based technique works best to link emails between threads while the combination of line-based and checksum-based technique achieves the best performance for linking emails in a thread with the final, accepted commit. Being able to reconstruct the full history of a patch allowed us to analyze the performance of the reviewing phase. We found that 25% of commits have a reviewing history longer than four weeks. To evaluate the ability of MSR to analyze the performance of Releng tools, we evaluated a hybrid integration approach, which combines branching and toggling techniques together, in a commercial project. Branching allows developers to work on different branches in parallel, while toggling enables developers on the same branch on different tasks. Instead of revising their whole integration process to drop branching and move to toggling, hybrid toggling is a compromise that tries to minimize the risks of branching while enjoy the benefits of toggling. We compared the performance before and after adopting hybrid toggling, and found that this hybrid structure can reduce integration effort and improve productivity. Hence, hybrid toggling seems a worthwhile practice. In the Provisioning phase, we focus on evaluating the usage and effort of the popular tools used in modern Release engineering: Infrastructure-as-Code (IaC). We empirically studied IaC tools in OpenStack and MediaWiki, which have a huge code base and adopt two currently most popular IaC languages: Puppet and Chef. First, we study maintenance effort related to the regular development and testing process of OpenStack, then compare this to IaC-related effort in both case studies. We found that IaC code takes a large proportion in both projects and it changes frequently, with large churn size. Meanwhile, IaC code changes are tightly coupled with source code changes, which implies that changes to source or test code require accompanying changes to IaC, which might lead to increased complexity and maintenance effort. Furthermore, the most common reason for such coupling is “Integration of new modules or service”. However, we also observed IaC code has light coupling with IaC test cases and test data, which are new kinds of artifacts in IaC domain. Hence, IaC may take more effort than engineers expect and further empirical studies should be considered. Modern Release engineering has developed rapidly, while many new techniques/tools emerge to support it from different perspectives. However, lack of knowledge of the current Release engineering progress and performance of these techniques makes it difficult for practitioners to sustain high quality Releng approach in practice. In this thesis, we conducted a series of empirical studies of mining software repositories of large open-source projects, that show that, despite some challenges, MSR technology can help release engineers understand better the progress of and evaluate the cost of Release engineering tools and activities. We are glad to see our work has inspired other researchers to further analyze the integration process as well as the quality of IaC code

Can Who-Edits-What Predict Edit Survival?

As the number of contributors to online peer-production systems grows, it becomes increasingly important to predict whether the edits that users make will eventually be beneficial to the project. Existing solutions either rely on a user reputation system or consist of a highly specialized predictor that is tailored to a specific peer-production system. In this work, we explore a different point in the solution space that goes beyond user reputation but does not involve any content-based feature of the edits. We view each edit as a game between the editor and the component of the project. We posit that the probability that an edit is accepted is a function of the editor's skill, of the difficulty of editing the component and of a user-component interaction term. Our model is broadly applicable, as it only requires observing data about who makes an edit, what the edit affects and whether the edit survives or not. We apply our model on Wikipedia and the Linux kernel, two examples of large-scale peer-production systems, and we seek to understand whether it can effectively predict edit survival: in both cases, we provide a positive answer. Our approach significantly outperforms those based solely on user reputation and bridges the gap with specialized predictors that use content-based features. It is simple to implement, computationally inexpensive, and in addition it enables us to discover interesting structure in the data.Comment: Accepted at KDD 201

An Historical Analysis of the SEAndroid Policy Evolution

Android adopted SELinux's mandatory access control (MAC) mechanisms in 2013. Since then, billions of Android devices have benefited from mandatory access control security policies. These policies are expressed in a variety of rules, maintained by Google and extended by Android OEMs. Over the years, the rules have grown to be quite complex, making it challenging to properly understand or configure these policies. In this paper, we perform a measurement study on the SEAndroid repository to understand the evolution of these policies. We propose a new metric to measure the complexity of the policy by expanding policy rules, with their abstraction features such as macros and groups, into primitive "boxes", which we then use to show that the complexity of the SEAndroid policies has been growing exponentially over time. By analyzing the Git commits, snapshot by snapshot, we are also able to analyze the "age" of policy rules, the trend of changes, and the contributor composition. We also look at hallmark events in Android's history, such as the "Stagefright" vulnerability in Android's media facilities, pointing out how these events led to changes in the MAC policies. The growing complexity of Android's mandatory policies suggests that we will eventually hit the limits of our ability to understand these policies, requiring new tools and techniques.Comment: 16 pages, 11 figures, published in ACSAC '1

SEKOLAH SEPAKBOLA USIA MUDA DI BANDA ACEH

Sepakbola merupakan olahraga yang sangat populer dan digemari di dunia, begitu juga di Indonesia. Tak heran jika hampir semua negara di dunia berlomba-lomba menggalang prestasi membanggakan di cabang olahraga ini. Indonesia belum mampu meraih prestasi yang membanggakan di cabang olahraga sepakbola, bahkan Indonesia sulit bersaing di kancah Internasional. Klub-klub sepakbola Aceh juga tidak dapat berbuat banyak di kompetisi internal, sedangkan Aceh merupakan salah satu provinsi yang banyak memunculkan pemain muda berbakat.Kualitas persepakbolaan di Indonesia yang rendah dan minim prestasi ini dikarenakan kurang pembinaan dan pelatihan pemain mulai dari usia dini untuk didik menjadi pemain profesional. Sarana pelatihan yang ada di Indonesia belum serius ke arah profesional seperti akademi sepakbola di Eropa. Di negara-negara maju dalam sepakbola, prestasi tim nasional pada umumnya dilatarbelakangi oleh sistem dan proses pembinaan klub yang sudah mapan.Sekolah sepakbola usia muda di Banda Aceh merupakan sebuah sarana pelatihan dan pembinaan sepakbola pemain usia dini di Banda Aceh. Pemain tersebut akan dididik, dilatih dan dibina sejak dini sebagai usaha pembibitan pemain sepakbola Aceh yang potensial. Sekolah sepakbola ini berlokasi di Lhong Raya, sesuai dengan rencana pengembangan kawasan pusat olahraga di Banda Aceh. Dengan mengusung tema arsitektur metafora, diharapkan bangunan sekolah sepakbola ini dapat menjadi objek arsitektur yang melekat di masyarakat.Tahap awal dalam proses perancangan Sekolah Sepakbola Usia Muda di Banda Aceh ini adalah studi literatur data dan studi banding. Selanjutnya permasalahan yang ada diidentifikasi dan dianalisis sesuai dengan batasan perancangan. Dalam lingkup batasan tema arsitektur metafora dan kondisi iklim setempat selanjutnya melahirkan konsep perancangan sesuai dengan hasil analisis.Kata kunci: olahraga, sekolah, sepakbolaBanda Ace

Detection of rubidium and samarium in the atmosphere of the ultra-hot Jupiter MASCARA-4b

Ultra-hot Jupiters (UHJs) possess the most extreme environments among various types of exoplanets, making them ideal laboratories to study the chemical composition and kinetics properties of exoplanet atmosphere with high-resolution spectroscopy (HRS). It has the advantage of resolving the tiny Doppler shift and weak signal from exoplanet atmosphere and has helped to detect dozens of heavy elements in UHJs including KELT-9b, WASP-76b, WASP-121b. MASCARA-4b is a 2.8-day UHJ with an equilibrium temperature of $\sim2250$ K, which is expected to contain heavy elements detectable with VLT. In this letter, we present a survey of atoms/ions in the atmosphere of the MASCARA-4b, using the two VLT/ESPRESSO transits data. Cross-correlation analyses are performed on the obtained transmission spectra at each exposure with the template spectra generated by petitRADTRANS for atoms/ions from element Li to U. We confirm the previous detection of Mg, Ca, Cr and Fe and report the detection of Rb, Sm, Ti+ and Ba+ with peak signal-to-noise ratios (SNRs) $>$ 5. We report a tentative detection of Sc+, with peak SNRs $\sim$6 but deviating from the estimated position. The most interesting discovery is the first-time detection of elements Rb and Sm in an exoplanet. Rb is an alkaline element like Na and K, while Sm is the first lanthanide series element and is by far the heaviest one detected in exoplanets. Detailed modeling and acquiring more data are required to yield abundance ratios of the heavy elements and to understand better the common presence of them in UHJ's atmospheres.Comment: 11 pages, 7 figures, Accepted to A

Evaluations of 5-fluorourcil treated lung cancer cells by atomic force microscopy

Atomic force microscopy (AFM) can be used to obtain the physical information of single live cancer cells; however, the physical changes in live cells with time based on AFM remain to be studied, which play a key role in the evaluation of the efficacy and side effects of drugs. Herein, the treatment of the A549 cell line with the anticarcinogen 5-fluorouracil has been discussed based on the AFM analysis of their continuous physical changes, including their surface morphology, height, adhesion and Young's modulus, with time. In comparison, the African green monkey kidney (Vero) cell line was tested as normal cells to determine the side effects of 5-fluorouracil. The results show that the optimal concentration of 5-fluorouracil is about 500 μM, which presents the best anticancer effect and mild side effects

Epidemiology of potential drug- drug interactions in hospitalized patients with type 2 diabetes mellitus in China: a retrospective study

BackgroundCombination therapy was associated with an increased risk of drug- drug interactions (DDIs) in patients with type 2 diabetes mellitus (T2DM). The present study aimed to investigate the epidemiology of potential DDIs (pDDIs), including potential chemical drug-drug interactions (pCDIs) and potential herb-drug interactions (pHDIs), and classify the influencing factors of pDDIs in these patients.MethodsA retrospective study of the epidemiology of pDDIs among T2DM hospitalized patients older than 18 years and treated with at least two drugs during hospitalization was conducted over a 12-month period in 2019. PDDIs were identified with C (monitor therapy), D (consider therapy modification), and X (avoid combination) risk ratings. Binary logistic regression was used to analyze the risk factors of pDDIs.ResultsA total of 6796 pDDIs were identified from 737 T2DM hospitalized patients during hospitalization, with 0.87% classified as X risk rating, 13.39% as D risk rating. Additionally, 1753 pDDIs were identified after discharge, with 0.11% as X and 25.73% as D risk rating. The drug-drug association networks showed that the majority of pCDIs were associated with cardiovascular system drugs. Chlorphenamine-potassium chloride and danshen-warfarin were the most prevalent interacting pairs of pCDIs and pHDIs with X rating during hospitalization. Multivariate analysis indicated that the likelihood of developing over 4 pDDIs was significantly higher among T2DM patients who had received over 8 medications. The presence of pDDIs after discharge was strongly associated with the complications of T2DM and the number of discharge medications.ConclusionsT2DM patients were frequently exposed to pDDIs, including pCDIs and pHDIs, both during hospitalization and after discharge. Multi-drug combination was the primary risk factor for pDDIs. Strategies such as enhancing the monitoring and warning for pDDIs, increasing clinical pharmacological experience, as well as developing universally applicable clinical guidelines for pDDIs may be beneficial in reducing the incidence of potentially harmful drug-combinations

Oncological and surgical outcomes of radical surgery in elderly colorectal cancer patients with intestinal obstruction

BackgroundThe treatment strategy for elderly colorectal cancer patients with intestinal obstruction remains controversial. The choice of reasonable treatment and surgical method directly affects perioperative safety and prognosis. This study investigated the safety and long-term efficacy of radical surgery in elderly colorectal cancer patients over 80 years old with intestinal obstruction.MethodsThe clinicopathological data of elderly patients over 80 years old with intestinal obstruction who underwent colorectal cancer surgery from January 2012 to December 2021 were retrospectively collected and analysed. Patients were assigned to a radical group and a palliative group according to the surgical method. Propensity score matching (PSM) was performed to match patients in the radical group 1:1 with those in the palliative group. The perioperative-related indexes and prognosis were compared between the two groups.ResultsA total of 187 patients were enrolled in this study. After PSM, 58 matched pairs were selected, and the radical and palliative groups were well balanced in terms of the clinical and surgical characteristics (P > 0.05). The proportion of patients transferred to the ICU after surgery in the radical group was significantly higher than that in the palliative group (17.2% vs. 5.2%, P = 0.039). In terms of postoperative complications, the incidence of grade 1–5 complications in the radical group was significantly higher than that in the palliative group (37.9% vs. 15.5%, P = 0.006); however, there was no significant difference in the incidence of grade 3–5 complications between the two groups (6.9% vs. 1.7%, P = 0.364). In addition, the complications were subclassified, and it was found that the incidence of gastrointestinal disorders (20.7% vs. 6.9%, P = 0.031) after surgery was significantly higher in the radical group. The 3-year OS rates were 55.2% and 22.6% in the radical and palliative groups, respectively (P < 0.001). Multivariate analysis revealed that radical surgery was an independent prognostic factor for OS (HR: 4.32; 95% CI, 1.93–12.45; P < 0.001).ConclusionAlthough elderly colorectal cancer patients over 80 years of age with intestinal obstruction are more likely to be admitted to the ICU and develop more postoperative complications after radical surgery, long-term survival benefits can be achieved

Altered Gut Microbiota Composition in Subjects Infected With Clonorchis sinensis

Clonorchiasis is an infectious disease caused by helminths of Clonorchis sinensis (C. sinensis). The adult parasite mainly inhabits the bile duct and gall bladder, and results in various complications to the hepatobiliary system. The amount of bile secreted into the intestine is reduced in cases of C. sinensis infection, which may alter the pH of the gut and decrease the amount of surfactant protein D released from the gallbladder. However, the impact of parasitic infection on the human gut microbiome remains unclear. To this end, we examined the gut microbiota composition in 47 modified Kato–Katz thick smear-positive (egg-positive) volunteers and 42 healthy controls from five rural communities. Subjects were grouped into four sub-populations based on age and infection status. High-throughput 16S rRNA gene sequencing revealed significant changes in alpha diversity between EP1 and EN1. The beta diversity showed alterations between C. sinensis-infected subjects and healthy controls. In C. sinensis infected patients, we found the significant reduction of certain taxa, such as Bacteroides and anti-inflammatory Bifidobacterium (P < 0.05). Bacteroides, a predominant gut bacteria in healthy populations, was negatively correlated with the number of C. sinensis eggs per gram (EPG, r = −0.37, P adjust < 0.01 in 20–60 years old group; r = −0.64, P adjust = 0.04 in the 60+ years old group). What’s more, the reduction in the abundance of Bifidobacterium, a common probiotic, was decreased particularly in the 60 + years old group (r = −0.50, P = 0.04). The abundance of Dorea, a potentially pro-inflammatory microbe, was higher in infected subjects than in healthy individuals (P < 0.05). Variovorax was a unique bacteria that was only detected in infected subjects. These results clearly demonstrate the significant influence of C. sinensis infection on the human gut microbiota and provided new insights into the control, prevention, diagnosis, and clinical study of clonorchiasis through the human gut microbiota

Mechanochemical synthesis of pillar[5]quinone derived multi-microporous organic polymers for radioactive organic iodide capture and storage.

The incorporation of supramolecular macrocycles into porous organic polymers may endow the material with enhanced uptake of specific guests through host-guest interactions. Here we report a solvent and catalyst-free mechanochemical synthesis of pillar[5]quinone (P5Q) derived multi-microporous organic polymers with hydrophenazine linkages (MHP-P5Q), which show a unique 3-step N2 adsorption isotherm. In comparison with analogous microporous hydrophenazine-linked organic polymers (MHPs) obtained using simple twofold benzoquinones, MHP-P5Q is demonstrated to have a superior performance in radioactive iodomethane (CH3I) capture and storage. Mechanistic studies show that the rigid pillar[5]arene cavity has additional binding sites though host-guest interactions as well as the halogen bond (-I⋯N = C-) and chemical adsorption in the multi-microporous MHP-P5Q mainly account for the rapid and high-capacity adsorption and long-term storage of CH3I