bluuebunny/crossref_metadata_2025 huggingface dataset:
Implementation of the inquiry model assisted with quick response code to improve students’ critical thinking skills
Authors: Irmi I , Hasan M , Gani A , Safrida S
Published: March 2020

This research was aimed to study the influence of inquiry learning model with assisted quick response code (QR code) to students’ critical thinking skill (CTS) in the learning of salt hydrolysis in one of the senior high school in Banda Aceh. The sample was collected by purposive sampling. The quasi-experiment method was implemented in two classes, accompanied by nonequivalent control group design. Two groups of students from different chemistry class were selected as sample. The results showed that the CTS of students who are taught using enquiry model has higher posttest score compared to control class. Moreover, the results revealed that the comparison of average N-gain for all CTS indicators was 42.37% for control class and 73.57% for experiment class. Statistical analysis with t-test on all CTS indicators showed that the value of t count > t table at α = 0.05. The conclusion of this study is the implementation of inquiry model with assisted QR code improves student’ CTS.
Constructivist based students’ worksheet development in learning environmental pollution
Authors: Munawwarah I , Khaldun I , Nurmaliah C
Published: March 2020

Students’ worksheet is one of the learning tools to achieve learning objectives, to simplify teaching and learning process. However, the frequently used worksheet at schools was adapted from textbook with the key answers’ availability. This research aims to develop constructivist-based students’ worksheet to be feasible and useable for learning of environmental pollution. The research was carried out using research and development method (R&D) with ADDIE model. The research was conducted at SMPN 4 Banda Aceh during the academic year 2017/2018 in class VII-2 and VII-3. Data were collected using students’ worksheet, written test and questionnaire and later the data were analysed with percentage equation. The finding exhibited that the constructivist-based students’ worksheet was very good in accordance with feasibility assessment validated within average score of 0.87. Besides, learning achievement was categorized as good with a percentage of 82.21%. The responses to the worksheet obtained average percentage of 72.8% (strongly agree); 26.5% (agree) and 0.7% (disagree). Based on the results, it can be concluded that the worksheet was excellent and feasible to be used to achieve success in learning as well as positive responses from students.
A systematic literature review of science teachers’ TPACK related to STEM in developing a TPACK-STEM scale
Authors: Iswadi  , Syukri M , Soewarno  , Yulisman H , Nurina CIE
Published: March 2020

The success of implementing STEM in learning activities must begin with increasing the teachers’ TPACK ability. However, information about TPACK and STEM is currently limited. Thus, this article aims to analyze articles related to TPACK and STEM and start the development of TPACK-STEM instruments. This study is a systematic literature review that conducted based on the PRISMA statement. Based on the search results, 21 search results were obtained. The results consist of 16 articles and 5 chapters. The analysis shows that the application of TPACK-STEM requires a complex process. There are three stages in implementing TPACK-STEM. First, the development of TPACK instrument. Second, the process of developing teachers’ TPACK-STEM ability. Third, the application of TPACK-based STEM learning to students. This information is the first step in developing the TPACK-STEM instrument.
Students’ ability in solving physics-analysis problem through the TAI type cooperative learning model
Authors: Syukri M , Murniati  , Soewarno S , Yanti Y , Halim L
Published: March 2020

This study aims to determine students’ learning ability in completing the questions of Physics-analysis through the TAI type cooperative learning model. The research design used was pre-experimental design of The One Group Pretest-Posttest Design. The research subjects consisted of 30 first-level students (15 years old). The data was the students’ problem sloving and collected through the instrument which is in the form of an essay tests that have been validated by two experts in the field of Physics. The responses were then assessed using the assessment rubric and then processed using the SPSS program to get the results of paired sample t-test analysis. The results of t-test calculations was t= -24.475, p < 0.00. The results showed that there were differences in students’ learning abilities to solving the physics-analysis problems during the pre-test and post-test, so the use of this learning model could improve the ability of students in solving the analysis problem of physics in the motion concept in physics lesson.
The effect of students self-efficacy on the learning outcomes in learning physics
Authors: Nurulwati N , Khairina L , Huda I
Published: March 2020

The progress of a country can be seen from the quality of its education. The quality of education also depends on various factors such as teacher quality, student achievement, quality of physical facilities and infrastructure, educational equity and the environment. This study aims to determine the effect of self-efficacy students on the learning outcomes of physics at state senior high school 1 Pintu Rime Gayo. The type of research is correlational research with quantitative approach. The population of this study were all students of state senior high school 1 Pintu Rime Gayo, as muny as 84 people and the sample was students of 11th grade state senior high school Negeri 1 Pintu Rime Gayo as many as 20 people. The research instruments were documentation, questionnaires and tests of physics learning outcomes. The technique of analysing t-test data. Based on the results of data analysis, it was concluded that there was a positive correlation between the effect of self-efficacy on student’s learning outcomes in physics at state senior high school 1 Pintu Rime Gayo.
The contribution of Internship toward soft skill competencies of pre-service teachers
Authors: Elisa  , Mutiara K , Hamid A , Syukri M , Mazlina H , Musdar
Published: March 2020

Teaching is a diverse performance and requires a variety of knowledge and several skills including soft skills. But soft skills are more difficult to do and to teach. Therefore, the internship is an alternative way to practice these skills to physics students in teacher training and education faculty. Thus, this study aims to identify the contribution of internship value to students’ soft skills competencies. The study applied a descriptive survey method. A total of 36 students from a public university in Banda Aceh were selected using a purposive sampling method. Instruments used for data collection were multiple-choice test questions related to students’ soft skill competencies and apprenticeship data. Data analysis was conducted using SPSS through product-moment correlation test and correlation coefficient formula. The results showed that the contribution of apprenticeship value to students’ soft skills competencies is 0.48% with a correlation coefficient of 0.022 (very weak). Hence, it is suggested that the learning process should be emphasized in direct practice so that more competencies can be developed by students graduating from physics education department.
The differences in physics learning outcomes based on gender after using blended problem-based learning model
Authors: Herliana F , Astra I M , Supriyati Y , Mazlina H , Musdar
Published: March 2020

Previous studies found that using e-learning to support Problem Based Learning can increase students’ learning outcomes. The increase of students’ learning outcomes has not been yet examined according to gender difference which can indicate the suitability of a learning model used by male and female students to enhance their learning outcomes. This study aims to examine the differences in physics learning outcomes at a public senior high school in Depok according to gender difference after using Blended Problem Based Learning model. This is an ex de facto study. The target population of this study was students of a public senior high school in Depok and the sample was grade ten students at a public senior high school in Depok. Samples were taken by purposive sampling. Data were collected from students’ learning outcomes grouped by gender difference, then analyzed using a two-tail test with the t-test formula. The results showed that there are no significant difference between male students’ learning outcomes and female students’ learning outcomes after using the Blended Problem Based Learning model at a public senior high school in Depok.
Improving high school students’ physic performance using science process skills
Authors: Diana N , Khaldun I , Nur S
Published: March 2020

This study is aimed to investigate the application of Science Process Skills (SPS) as the scientific skills that could use to develop and increase science process skills and understanding of physics subject through laboratory activity. This study utilized experimental design by involving students grade ten-3 from Senior High School Banda Aceh academic year 2018/2019 as a sample. It followed the competence standard of 2013 Indonesian Curriculum. This study found that there was a positive correlation between the content of physics syllabus and the science process skills. This condition had contributed positively to students’ learning achievements. It could be seen from the result of pre and post-test where the result of post-test had improved after applying this approach. The research method used was the quasi-experimental with pretest-posttest one group design and observation sheets to observe the implementation of the learning method. Data processing was done by test obtained by the percentage of the average value of the initial test 60.33%. Then the final percentage average score was 82.33%. The result there was a significant change in student’s average value of learning outcomes on the post-test higher than the pre-test.
Direct instruction model assisted with PhET and Whatsapp to students’ cognitive and motivation
Authors: Oktavia F , Muhibbuddin  , Mursal
Published: March 2020

This research aims at understanding the influence of the direct instruction learning model assisted with PhET and WhatsApp media to students’ cognitive and motivation in studying gas kinetic theory at State Senior High School 3 of Banda Aceh. The population in this study was all science department students at year 11 divided into 5 classes. While the sample of the study was two classes that were selected using a random sampling technique. Data were collected by providing test and non-test. The obtained data were normal and homogeneous. Thus, it can be analyzed using the t-test to measure learning outcomes. To indicate the difference between experimental class and control class, it was used the t-test for questionnaire. Pretest has ttest = 1.27 which its value is less than ttable. In conclusion, there is any significant difference between the experimental class and the control class. In addition, both classes revealed the same difference for the pretest. The posttest also showed the significant difference according to tcount = 5.5 which is greater than ttable. Therefore, it can be concluded that there is any difference, which students’ cognitive experimental class is greater than the control class.
The impact of the media tracker on student critical thinking skills
Authors: Wati S , Halim A , Mustafa
Published: March 2020

This research aims to determine the impact of media tracker on students’ critical thinking skills in the concept of free fall motion and responses of students to the media tracker. The method used in this research is the pre-experimental design method through one group pretest-posttest design, the research design that gives treatment to the experimental group without being compared with the control group. The type of approach used is a quantitative approach. The population of this research was all students of grade ten of Senior High School 3 Banda Aceh, while the sample was 30 students which were randomly selected. The treatment in the sample class is learning using a media tracker. Data collection uses essay tests and student response questionnaires developed by researchers. The results of data analysis with descriptive statistics indicate that there is an influence of tracker learning media on improving critical thinking skills with an N-gain value of 0.68 in the medium category. Besides that, learning using media tracker gets a positive response from students. Inference from the results of this study, teachers are expected to be able and willing to apply the media tracker on temperature and heat learning or other concepts in physics.
The development of higher order thinking skills (HOTS) questions for static fluid concept
Authors: Rizki M , Sulastri  , Mursal
Published: March 2020

The achievements of Indonesian students at TIMMS are still categorized low. One of the reasons is that students are poorly trained in solving HOTS problems. The observations showed that questions used in the 2017/2018 odd semester exam in high schools in Banda Aceh were still categorized as LOTS, so giving HOTS questions has become a necessity. The purpose of this study was to develop and analyze HOTS questions on static fluid materials. The method used was research and development (R&D) with the ADDIE model. The number of samples was 66 students who were selected using a random sampling technique. The data were collected through questionnaires and written tests. The average percentage of expert validation was 97.98% which indicated a very decent category. The quality of the HOTS question test obtained 16 (20%) valid items and 4 (20%) invalid items. The reliability was 0.878 which indicated a very high category. The test item difficulty index consisted of 6 difficult items, 9 moderate items and 5 easy items. The confounders as much as 92.25% worked well and 8.75% did not work. It can be concluded that the questions from the results of this development can be used to train students HOTS.
The development of student worksheets with PhET assisted to improve student science process skill
Authors: Arifullah  , Halim A , Syukri M , Nurfadilla E
Published: March 2020

The purpose of this study is to develop worksheet based on computer simulation (PhET), and to investigate the contribution of that worksheet in increasing students’ science process skill in learning physics especially for Hooke law concept. Worksheet developed for senior high school level used Research and Development approach with ADDIE model, and has already declared by the validator. Design and method used in this research was with matching pretest-posttest one group design. The research population conducted in one of private Senior High School located at Public Senior High School 1 Peukan Baro Pidie, this random sampling for research is done in grade eleven 4. As a result of this research, it was found that the science process skill of the experimental group was significantly higher than before, it means the developed worksheet can be effectively used to increase students’ science process skills.
Physical and chemical properties of particleboard made of rice straw and plastic waste
Authors: Fitri N , Mursal  , Ismail I
Published: March 2020

Rice straw is agricultural waste which hasn’t been used optimally yet, especially in Indonesia. Meanwhile, rice straw contains cellulose that can be used form composite such particleboard. In this study, the physical and chemical properties of particleboard made of rice straw particle and polypropylene from plastic waste as adhesive were investigated. The rice straw and polypropylene compositions were varied: 30:70, 40:60, 50:50, and 60:40 wt.%. The rice straw particle sizes were varied for 40 mesh, 50 mesh, and 60 mesh for each composition. X-Ray Fluorescent has been used to measure the chemical composition of our particleboard. The density of particleboard is 0.59-0.77 g / cm3. Its thickness swelling is less than 2%. Both density and thickness swelling has met the requirement for Indonesian Standard of particleboard. Our results showed that the density of particleboard strongly depends on rice straw particle size. As the particle size decreases, the density increases. The particle size of rice straw affects the thickness swelling of particleboard. The thickness swelling decreases as the particle size decreases. The major constituents of our particleboard are the SiO2, CaO, K2O. Our finding showed that the particle size has an essential role in the physical properties of particleboard.
The architectural transformation of historic mosques in Javanese rural settlements
Authors: Hidayati R , Setiawan W
Published: March 2020

The formation of traditional Javanese villages often began with the establishment of a center for activity, generally a traditional mosque. Currently, several historic mosques in rural areas have survived with various changes. This study aims to explore the trends in the transformation of mosques. The research focuses on the area around Jatinom Village, Klaten, which is famous for its Islamic and Javanese culture. It assesses five historic mosques in the villages of Jatinom, Kadirejo, and Belangwetan. The research adopts a comparative case study method using observations, literature review, and interviews. The results show that (1) the mosques have changed from its traditional form; (2) four elements remain the same: the 2-3-tiered roof shape, the soko guru structure, the mihrab, and the main three doors in the front façade; and (3) two elements mostly change: the façade and the terrace. Understanding this trend would help the community to anticipate in preserving the historic mosques.
Desertification categorisation based on spatial analysis and remote sensing technology
Authors: Shihab Tay H , AL-Hameedawi Amjed N M , Hamza Ammar M
Published: March 2020

This paper illustrates techniques based on multi-criteria evaluation for categorising desertification in the north-west of Iraq. Desertification is recognised as not only one of the major dilemma threatening human communities but also reduces productivity such that the whole economy is affected. The aim of this paper is to produce a desertification map for the study area that identifies risk zones through modelling and mapping by using Analytical Hierarchy Process (AHP), which is one of the Multiple Criteria Decision Making, based GIS for the selection process. In order to produce a desertification categorisation for the study area, numbers of criteria were identified depending on the questionnaires provided by experts. The produced desertification hazard map shown in ‘figure 3 indicates that 3.98% of the area is under very high sensitivity to desertification. The remaining area under high sensitivity is 7.25% and moderate sensitivity is 25.97%. The most hazardous areas are found in the middle and south parts of the study area. This paper including its methodology can be extrapolated to different desertification problems.
The Distribution of Accidents and Work Injuries using GIS technique: Baghdad as a Case Study
Authors: Abduljabbar Tamarah S. , Saad Fouad H.
Published: March 2020

The research involved collect data through data extraction from satellite images, spatial and non-spatial data which provide from field survey that used in design of geodatabase and digital maps for study area through last three years (2015-2017) to record the frequency of work injuries occurring in Baghdad and spatial distribution for these work injuries. On the other side this research maintain the issue of losses the efforts of awareness teams which work with national center of occupational safety and health through apply GIS technique help the planners to prepare focused and effective plans through benefit from the spatial distribution of accident and work injuries to publish the knowledge of occupational safety and health between the labors in private sector according to how extent the types and numbers of work injuries. Also the research involved building geodatabase for the locations of governmental hospitals which covered by the system of monitoring and recording work injuries and spatial analysis for the types and numbers of work injuries by using satellite images and ArcGIS program to produce cartography maps involved the numerous classifications in addition to display the spatial relationship between the industrial activities and the type of work injuries in Baghdad area.
Finite gap conditions and small dispersion asymptotics for the classical periodic Benjamin–Ono equation
Authors: Moll Alexander
Published: March 2020

In this paper we characterize the Nazarov–Sklyanin hierarchy for the classical periodic Benjamin–Ono equation in two complementary degenerations: for the multiphase initial data (the periodic multisolitons) at fixed dispersion and for bounded initial data in the limit of small dispersion. First, we express this hierarchy in terms of a piecewise-linear function of an auxiliary real variable which we call adispersive action profileand whose regions of slope±1\pm 1we call gaps and bands, respectively. Our expression uses Kerov’s theory of profiles and Kreĭn’s spectral shift functions. Next, for multiphase initial data, we identify Baker–Akhiezer functions in Dobrokhotov–Krichever and Nazarov–Sklyanin and prove that multiphase dispersive action profiles have finitely many gaps determined by the singularities of their Dobrokhotov–Krichever spectral curves. Finally, for bounded initial data independent of the coefficient of dispersion, we show that in the small dispersion limit, the dispersive action profile concentrates weakly on a convex profile which encodes the conserved quantities of the dispersionless equation. To establish the weak limit, we reformulate Szegő’s first theorem for Toeplitz operators using spectral shift functions. To illustrate our results, we identify the dispersive action profile of sinusoidal initial data with a profile found by Nekrasov–Pestun–Shatashvili and its small dispersion limit with the convex profile found by Vershik–Kerov and Logan–Shepp.
Julia sets as buried Julia components
Authors: Wang Youming , Yang Fei
Published: March 2020

Let

f
f

be a rational map with degree

d
≥
2

d\geq 2

whose Julia set is connected but not equal to the whole Riemann sphere. It is proved that there exists a rational map

g
g

such that

g
g

contains a buried Julia component on which the dynamics is quasiconformally conjugate to that of

f
f

on the Julia set if and only if

f
f

does not have parabolic basins and Siegel disks. If such

g
g

exists, then the degree can be chosen such that

deg
⁡
(
g
)
≤
7
d
−
2

\deg (g)\leq 7d-2

. In particular, if

f
f

is a polynomial, then

g
g

can be chosen such that

deg
⁡
(
g
)
≤
4
d
+
4

\deg (g)\leq 4d+4

. Moreover, some quartic and cubic rational maps whose Julia sets contain buried Jordan curves are also constructed.
Poor Awareness of Hypertension in France: The CONSTANCES Population-Based Study
Authors: Fenech Goël , Vallée Alexandre , Cherfan Michelle , Kab Sofiane , Goldberg Marcel , Zins Marie , Blacher Jacques
Published: March 2020

OBJECTIVES

We aimed to assess the hypertension (HTN) awareness and associated factors in France.

METHODS

We conducted a cross-sectional analysis using data from the CONSTANCES population-based cohort involving 87,808 volunteer participants included between 2012 and 2018. HTN was defined as average blood pressure (BP) over 140/90 or use of BP medication, awareness as self-reported HTN. Multivariable logistic regression models were used to identify the associated factors.

RESULTS

Overall, 27,160 hypertensive participants (men = 16,569) above 18 years old were analyzed. Hypertension awareness rate was 37.5%. In the multivariable regression model, awareness was predicted by female gender, age, prior cardiovascular disease (CVD), presence of diabetes mellitus (DM), presence of chronic kidney disease (CKD), level of education, and obesity or overweight. Older participants (P < 0.001), females (P < 0.001), participants with comorbidities (P < 0.001), were more likely to be aware when compared with younger participants, males and participants without comorbidities, respectively. The unawareness among participants without cardiometabolic factors (CMF, i.e., CVD, DM, CKD) was higher than participants with CMF (67% vs. 41%, respectively, P < 0.001). Moreover, some differences appeared in both genders in the association between awareness of HTN and health and lifestyle factors.

CONCLUSION

Our findings show that HTN awareness is low. Particular attention should be given to young men without comorbidities as these characteristics were predictors of poor awareness. Immediate action is required to improve HTN awareness in France.
Alcohol Consumption by Older New York City Residents: The Need for New Policies to Address Misuse
Authors: Weisz Daniel , Gusmano Michael Kelley
Published: March 2020

Aims

The aim of this study is to assess risk factors for alcohol misuse among older New York City residents and examine the effect of local public health efforts to address alcohol misuse.

Methods

The Community Health Survey, a cross-sectional telephone survey of 8500 randomly selected adult New Yorkers, records the frequency of alcohol use. We examine these results among 65 and older subjects by sociodemographic status using logistic regression modeling and compare trends in smoking and alcohol consumption between 2002 and 2016.

Results

Those with unhealthy drinking habits, combining binge drinking and excessive consumption, constituted 5.7% of 65 plus population and were more likely to be White, US born, healthy, better educated and wealthier. The percentage of older smokers in New York City has decreased while unhealthy drinking is nearly flat since 2002.

Conclusions

Our findings reinforce the importance of screening geriatric populations for alcohol use disorders and support the development of new public health efforts to address alcohol misuse if the city is to achieve results similar to those obtained in decreasing tobacco consumption.
Unified methods for feature selection in large-scale genomic studies with censored survival outcomes
Authors: Spirko-Burns Lauren , Devarajan Karthik
Published: March 2020

Motivation

One of the major goals in large-scale genomic studies is to identify genes with a prognostic impact on time-to-event outcomes which provide insight into the disease process. With rapid developments in high-throughput genomic technologies in the past two decades, the scientific community is able to monitor the expression levels of tens of thousands of genes and proteins resulting in enormous datasets where the number of genomic features is far greater than the number of subjects. Methods based on univariate Cox regression are often used to select genomic features related to survival outcome; however, the Cox model assumes proportional hazards (PH), which is unlikely to hold for each feature. When applied to genomic features exhibiting some form of non-proportional hazards (NPH), these methods could lead to an under- or over-estimation of the effects. We propose a broad array of marginal screening techniques that aid in feature ranking and selection by accommodating various forms of NPH. First, we develop an approach based on Kullback–Leibler information divergence and the Yang–Prentice model that includes methods for the PH and proportional odds (PO) models as special cases. Next, we propose R2 measures for the PH and PO models that can be interpreted in terms of explained randomness. Lastly, we propose a generalized pseudo-R2 index that includes PH, PO, crossing hazards and crossing odds models as special cases and can be interpreted as the percentage of separability between subjects experiencing the event and not experiencing the event according to feature measurements.

Results

We evaluate the performance of our measures using extensive simulation studies and publicly available datasets in cancer genomics. We demonstrate that the proposed methods successfully address the issue of NPH in genomic feature selection and outperform existing methods.

Availability and implementation

R code for the proposed methods is available at github.com/lburns27/Feature-Selection.

Contact

karthik.devarajan@fccc.edu

Supplementary information

Supplementary data are available at Bioinformatics online.
iATC-FRAKEL: a simple multi-label web server for recognizing anatomical therapeutic chemical classes of drugs with their fingerprints only
Authors: Zhou Jian-Peng , Chen Lei , Wang Tianyun , Liu Min
Published: March 2020

Motivation

Anatomical therapeutic chemical (ATC) classification system is very important for drug utilization and studies. Correct prediction of the 14 classes in the first level for given drugs is an essential problem for the study on such system. Several multi-label classifiers have been proposed in this regard. However, only two of them provided the web servers and their performance was not very high. On the other hand, although some rest classifiers can provide better performance, they were built based on some prior knowledge on drugs, such as information of chemical–chemical interaction and chemical ontology, leading to limited applications. Furthermore, provided codes of these classifiers are almost inaccessible for pharmacologists.

Results

In this study, we built a simple web server, namely iATC-FRAKEL. This web server only required the SMILES format of drugs as input and extracted their fingerprints for making prediction. The performance of the iATC-FRAKEL was much higher than all existing web servers and was comparable to the best multi-label classifier but had much wider applications. Such web server can be visited at http://cie.shmtu.edu.cn/iatc/index.

Availability and implementation

The web server is available at http://cie.shmtu.edu.cn/iatc/index.

Contact

chen_lei1@163.com

Supplementary information

Supplementary data are available at Bioinformatics online.
More efficient approximation of smoothing splines via space-filling basis selection
Authors: Meng Cheng , Zhang Xinlian , Zhang Jingyi , Zhong Wenxuan , Ma Ping
Published: March 2020

We consider the problem of approximating smoothing spline estimators in a nonparametric regression model. When applied to a sample of size $n$, the smoothing spline estimator can be expressed as a linear combination of $n$ basis functions, requiring $O(n^3)$ computational time when the number $d$ of predictors is two or more. Such a sizeable computational cost hinders the broad applicability of smoothing splines. In practice, the full-sample smoothing spline estimator can be approximated by an estimator based on $q$ randomly selected basis functions, resulting in a computational cost of $O(nq^2)$. It is known that these two estimators converge at the same rate when $q$ is of order $O\{n^{2/(pr+1)}\}$, where $p\in [1,2]$ depends on the true function and $r > 1$ depends on the type of spline. Such a $q$ is called the essential number of basis functions. In this article, we develop a more efficient basis selection method. By selecting basis functions corresponding to approximately equally spaced observations, the proposed method chooses a set of basis functions with great diversity. The asymptotic analysis shows that the proposed smoothing spline estimator can decrease $q$ to around $O\{n^{1/(pr+1)}\}$ when $d\leq pr+1$. Applications to synthetic and real-world datasets show that the proposed method leads to a smaller prediction error than other basis selection methods.
Robust estimation of causal effects via a high-dimensional covariate balancing propensity score
Authors: Ning Yang , Sida Peng , Imai Kosuke
Published: March 2020

We propose a robust method to estimate the average treatment effects in observational studies when the number of potential confounders is possibly much greater than the sample size. Our method consists of three steps. We first use a class of penalized $M$-estimators for the propensity score and outcome models. We then calibrate the initial estimate of the propensity score by balancing a carefully selected subset of covariates that are predictive of the outcome. Finally, the estimated propensity score is used to construct the inverse probability weighting estimator. We prove that the proposed estimator, which we call the high-dimensional covariate balancing propensity score, has the sample boundedness property, is root-$n$ consistent, asymptotically normal, and semiparametrically efficient when the propensity score model is correctly specified and the outcome model is linear in covariates. More importantly, we show that our estimator remains root-$n$ consistent and asymptotically normal so long as either the propensity score model or the outcome model is correctly specified. We provide valid confidence intervals in both cases and further extend these results to the case where the outcome model is a generalized linear model. In simulation studies, we find that the proposed methodology often estimates the average treatment effect more accurately than existing methods. We also present an empirical application, in which we estimate the average causal effect of college attendance on adulthood political participation. An open-source software package is available for implementing the proposed methodology.
Transplanted Embryonic Neurons Improve Functional Recovery by Increasing Activity in Injured Cortical Circuits
Authors: Andreoli Evgenia , Petrenko Volodymyr , Constanthin Paul Eugène , Contestabile Alessandro , Bocchi Riccardo , Egervari Kristof , Quairiaux Charles , Salmon Patrick , Kiss Jozsef Zoltan
Published: March 2020

Transplantation of appropriate neuronal precursors after injury is a promising strategy to reconstruct cortical circuits, but the efficiency of these approaches remains limited. Here, we applied targeted apoptosis to selectively ablate layer II/III pyramidal neurons in the rat juvenile cerebral cortex and attempted to replace lost neurons with their appropriate embryonic precursors by transplantation. We demonstrate that grafted precursors do not migrate to replace lost neurons but form vascularized clusters establishing reciprocal synaptic contacts with host networks and show functional integration. These heterotopic neuronal clusters significantly enhance the activity of the host circuits without causing epileptic seizures and attenuate the apoptotic injury-induced functional deficits in electrophysiological and behavioral tests. Chemogenetic activation of grafted neurons further improved functional recovery, and the persistence of the graft was necessary for maintaining restored functions in adult animals. Thus, implanting neuronal precursors capable to form synaptically integrated neuronal clusters combined with activation-based approaches represents a useful strategy for helping long-term functional recovery following brain injury.
ENaC-Dependent Sodium Chloride Taste Responses in the Regenerated Rat Chorda Tympani Nerve After Lingual Gustatory Deafferentation Depend on the Taste Bud Field Reinnervated
Authors: Jiang Enshe , Blonde Ginger D , Garcea Mircea , Spector Alan C
Published: March 2020

The chorda tympani (CT) nerve is exceptionally responsive to NaCl. Amiloride, an epithelial Na+ channel (ENaC) blocker, consistently and significantly decreases the NaCl responsiveness of the CT but not the glossopharyngeal (GL) nerve in the rat. Here, we examined whether amiloride would suppress the NaCl responsiveness of the CT when it cross-reinnervated the posterior tongue (PT). Whole-nerve electrophysiological recording was performed to investigate the response properties of the intact (CTsham), regenerated (CTr), and cross-regenerated (CT-PT) CT in male rats to NaCl mixed with and without amiloride and common taste stimuli. The intact (GLsham) and regenerated (GLr) GL were also examined. The CT responses of the CT-PT group did not differ from those of the GLr and GLsham groups, but did differ from those of the CTr and CTsham groups for some stimuli. Importantly, the responsiveness of the cross-regenerated CT to a series of NaCl concentrations was not suppressed by amiloride treatment, which significantly decreased the response to NaCl in the CTr and CTsham groups and had no effect in the GLr and GLsham groups. This suggests that the cross-regenerated CT adopts the taste response properties of the GL as opposed to those of the regenerated CT or intact CT. This work replicates the 5 decade-old findings of Oakley and importantly extends them by providing compelling evidence that the presence of functional ENaCs, essential for sodium taste recognition in regenerated taste receptor cells, depends on the reinnervated lingual region and not on the reinnervating gustatory nerve, at least in the rat.
First Case of Invasive Stachybotrys Sinusitis
Authors: Semis Margarita , Dadwal Sanjeet S , Tegtmeier Bernard R , Wilczynski Sharon P , Ito James I , Kalkum Markus
Published: March 2020

Background

The toxigenic mold Stachybotrys has controversially been linked to idiopathic pulmonary hemorrhage and “sick building syndrome.” However, there are no previous clinical records of invasive stachybotryosis.

Methods

Sinus biopsy specimens from a 23-year-old male with refractory acute lymphocytic leukemia were obtained at 3 different time points during the patient’s hospitalization (139 days) and examined by histopathology and immunohistochemistry (IHC). Antifungal susceptibility testing and fungal speciation using multilocus sequence typing were performed.

Results

Hemorrhage, fungal germination, and hyphal growth were observed in the first sinus biopsy tissues. Areas with fungal growth tested positive for Stachybotrys by IHC. Fungal isolates were genotyped and identified as Stachybotrys chlorohalonata. The patient was cured from Stachybotrys sinusitis following sinus surgery and antifungal treatment. While a subsequent second sinus biopsy and a bronchoscopy showed no signs of fungal infection, a later, third sinus biopsy tested positive for Aspergillus calidoustus, a rare human pathogen.

Conclusions

Here, we report the first case of invasive S. chlorohalonata sinusitis that was surgically and medically cured but followed by invasive A. calidoustus sinusitis in the setting of refractory leukemia. Our findings emphasize the risk for unusual fungal infections in severely immunocompromised patients.
Management of Rectal Stump During Laparoscopic Subtotal Colectomy for Inflammatory Bowel Disease: A Comparative Cohort Study from Six Referral Centres
Authors: Mege Diane , Stellingwerf Merel E , Germain Adeline , Colombo Francesco , Pellino Gianluca , Di Candido Francesca , Maggiori Léon , Foschi Diego , Buskens Christianne J , Adegbola Samuel , Spinelli Antonino , Warusavitarne Janindra , Bemelman Willem A , Sampietro Gianluca , D’Hoore André , Panis Yves
Published: March 2020

Background and Aims

There is no consensus on the best management of the rectum after subtotal colectomy for refractory colitis complicating inflammatory bowel disease [IBD]. The objective was to evaluate the impact of rectal stump management during laparoscopic subtotal colectomy [LSTC] for IBD.

Methods

Patients who underwent LSTC with double-end ileo-sigmoidostomy [Gr.A] or end ileostomy with closed rectal stump [Gr.B] for IBD were included from a retrospective database of six European referral centres.

Results

In total, 314 patients underwent LSTC and were allocated to Gr.A [n = 102] and B [n = 212]. After LSTC, stoma-related complications occurred more frequently in Gr.A [12%] than in Gr.B [4%, p = 0.01]. Completion proctectomy with ileal pouch-anal anastomosis [IPAA] was performed as a three-stage procedure in all patients from Gr.A, and in 88 patients from Gr.B [42%; Gr.B1]. The other 124 patients from Gr.B underwent a modified two-stage procedure [58%; Gr.B2]. The second stage was performed laparoscopically in all patients from Gr.A compared with 73% of Gr.B1 [p < 0.0001] and 65% of Gr.B2 patients [p < 0.0001]. When laparoscopy was intended for 2nd stage IPAA, conversion to laparotomy occurred less frequently in Gr.A when compared with B1 [0 vs 5%, p = 0.06] or B2 [10%, p = 0.001]. When all surgical stages were included [LSCT and IPAA], cumulative stoma-related complications occurred more frequently in Gr.A [n = 19] than in Gr.B1 [n = 6, p = 0.02] and Gr.B2 [n = 6, p = 0.001].

Conclusion

This study suggests that both techniques of double-end ileosigmoidostomy and end ileostomy with closed rectal stump are safe and effective for rectal stump management after laparoscopic subtotal colectomy.
Discovering and genotyping genomic structural variations by yeast genome synthesis and inducible evolution
Authors: Chen Si , Xie Ze-Xiong , Yuan Ying-Jin
Published: March 2020

Genomic structural variations (SVs) promote the evolution of Saccharomyces cerevisiae, and play an important role in phenotypic diversities. Yeast genomic structures can be remodeled by design and bottom-up synthesis. The synthesis of yeast genome creates novel copy number variations (CNVs) and SVs and develops new strategies to discover gene functions. Further, an inducible evolution system SCRaMbLE, consisted of 3,932 loxPsym sites, was incorporated on synthetic yeast genome. SCRaMbLE enables genomic rearrangements at will and rapidly generates chromosomal number variations, and massive SVs under customized conditions. The impacts of genetic variations on phenotypes can be revealed by genome analysis and chromosome restructuring. Yeast genome synthesis and SCRaMbLE provide a new research paradigm to explore the genotypic mechanisms of phenotype diversities, and can be used to improve biological traits and optimize industrial chassis.
Secondary Evolve and Resequencing: An Experimental Confirmation of Putative Selection Targets without Phenotyping
Authors: Burny Claire , Nolte Viola , Nouhaud Pierre , Dolezal Marlies , Schlötterer Christian
Published: March 2020

Evolve and resequencing (E&R) studies investigate the genomic responses of adaptation during experimental evolution. Because replicate populations evolve in the same controlled environment, consistent responses to selection across replicates are frequently used to identify reliable candidate regions that underlie adaptation to a new environment. However, recent work demonstrated that selection signatures can be restricted to one or a few replicate(s) only. These selection signatures frequently have weak statistical support, and given the difficulties of functional validation, additional evidence is needed before considering them as candidates for functional analysis. Here, we introduce an experimental procedure to validate candidate loci with weak or replicate-specific selection signature(s). Crossing an evolved population from a primary E&R experiment to the ancestral founder population reduces the frequency of candidate alleles that have reached a high frequency. We hypothesize that genuine selection targets will experience a repeatable frequency increase after the mixing with the ancestral founders if they are exposed to the same environment (secondary E&R experiment). Using this approach, we successfully validate two overlapping selection targets, which showed a mutually exclusive selection signature in a primary E&R experiment of Drosophila simulans adapting to a novel temperature regime. We conclude that secondary E&R experiments provide a reliable confirmation of selection signatures that either are not replicated or show only a low statistical significance in a primary E&R experiment unless epistatic interactions predominate. Such experiments are particularly helpful to prioritize candidate loci for time-consuming functional follow-up investigations.
A least-squares method for estimating the correlated error of GRACE models
Authors: Crowley John W , Huang Jianliang
Published: March 2020

A new least-squares method is developed for estimating and removing the correlated errors (stripes) from the Gravity Recovery and Climate Experiment (GRACE) and GRACE Follow-On (GRACE-FO) mission data. This method is based on a joint parametric model of the correlated errors and temporal trends in the spherical harmonic coefficients of GRACE models. Three sets of simulation data are created from the Global Land Data Assimilation System (GLDAS), the Regional Atmospheric Climate Model 2.3 (RACMO2.3) and GRACE models and used to test it. The results show that the new method improves the decorrelation method by Swenson & Wahr significantly. Its application to the release 5 (RL05) and new release 6 (RL06) spherical harmonic solutions from the Center for Space Research (CSR) at The University of Texas at Austin demonstrates its effectiveness and provides a relative assessment of the two releases. A comparison to the Swenson & Wahr and Kusche et al. methods highlights the deficiencies in past destriping methods and shows how the inclusion and decoupling of temporal trends helps to overcome them. A comparison to the CSR mascon and JPL mascon solutions demonstrates that the new method yields global trends that have greater amplitude than those produced by the CSR RL05 mascon solution and are of comparable quality to the JPL RL06 mascon solution. Furthermore, these results are obtained without the need for a priori information, scale factors or complex regularization methods and the solutions remain in the standard form of spherical harmonics rather than discrete mascons. The latter could introduce additional discretization error when converting to the spherical harmonic model, upon which many post-processing methods and applications are built.
Improved infrasound array processing with robust estimators
Authors: Bishop Jordan W , Fee David , Szuberla Curt A L
Published: March 2020

Infrasound array data are commonly used to detect and characterize infrasonic signals from a variety of natural and anthropogenic sources. Here we examine the effectiveness of robust regression estimators (L1-norm regression, M-estimators and least trimmed squares) for infrasound array processing, and compare them against standard array processing algorithms (least-squares estimation, frequency–wavenumber analysis and progressive multi-channel correlation) using a combination of real and synthetic data. Of particular interest is how each algorithm performs when one of the array elements produces data outliers. Synthetic tests on elements containing a clock error, constant values or only pink noise are performed, and we analyse the relative ability of the estimators to recover plane wave parameters. The L1-norm regression, M-estimate, frequency–wavenumber analysis and least trimmed squares estimates provided superior results than conventional least-squares estimation. Evaluation of least trimmed squares weights consistently identified the element with the simulated error, providing additional information on array performance. Least trimmed squares processing consistently identified an element with reversed polarity for Alaska Volcano Observatory array ADKI. International Monitoring System stations IS57 and IS55 were likewise processed. Data from an element of IS57, which had lower cross-correlation values than the remaining elements, were consistently identified as having outliers in array processing. An element with a timing error was identified in the analysis of IS55 data. These results suggest robust regression methods, in particular least trimmed squares, improve upon standard methods and should be used more widely, as they can provide robust array processing results and insight into array performance. Further, robust regression methods are not limited to infrasound array processing applications, and it is likely that they would also be effective for seismic array data.