bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fluent genomics with plyranges and tximeta
Authors: Lee Stuart , Lawrence Michael , Love Michael I. 
Published: February 2020

We construct a simple workflow for fluent genomics data analysis using the R/Bioconductor ecosystem. This involves three core steps: import the data into an appropriate abstraction, model the data with respect to the biological questions of interest, and integrate the results with respect to their underlying genomic coordinates. Here we show how to implement these steps to integrate published RNA-seq and ATAC-seq experiments on macrophage cell lines. Using tximeta, we import RNA-seq transcript quantifications into an analysis-ready data structure, called the SummarizedExperiment, that contains the ranges of the reference transcripts and metadata on their provenance. Using SummarizedExperiments to represent the ATAC-seq and RNA-seq data, we model differentially accessible (DA) chromatin peaks and differentially expressed (DE) genes with existing Bioconductor packages. Using plyranges we then integrate the results to see if there is an enrichment of DA peaks near DE genes by finding overlaps and aggregating over log-fold change thresholds. The combination of these packages and their integration with the Bioconductor ecosystem provide a coherent framework for analysts to iteratively and reproducibly explore their biological data.
PENINGKATAN DISPOSISI MATEMATIS DAN PRESTASI BELAJAR MATEMATIKA MELALUI PEMBELAJARAN TIPE AIR (AUDITORY, INTELECTUALLY, REPETITION)
Authors: Kurnia Esti , Fitrianawati Meita 
Published: February 2020

AbstrakPenelitian ini di latar belakangi yaitu masih menggunakan model pembelajaran ceramah dimana guru menjelaskan materi di depan kelas lalu memberi contoh soal kepada siswa. Selain itu, dapat dilihat bahwa suasana pembelajaran di kelas masih kurang kondunsif. Siswa masih kurang aktif dan kurang berpartisipasi dalam mengikuti pembelajaran. Sedangkan untuk prestasi belajar dapat dilihat dari hasil ulangan harian yang menunjukkan nilai rata-rata siswa masih banyak yang belum mendapatkan nilai dibatas yang ditentukan. Jenis penelitian ini adalah penelitian tindakan kelas (PTK) , dengan desain penelitian Kemmis dan Mc. Taggart yang meliputi perencanaan, pelaksanaan, pengamatan dan refleksi. Penelitian ini menggunakan dua siklus dengan setiap siklus ada dua kali pertemuan, sehingga dalam penelitian ini ada empat kali pertemuan. Subjek penelitian yaitu siswa kelas III yang berjumlah 25 siswa, dan objek penelitian yaitu disposisi matematis dan prestasi belajar matematika. Teknik pengumpulan data data menggunakan metode observasi, tes, dan dokumentasi. Hasil penelitian ini menunjukkan peningkatan pada siklus I dari aspek disposisi matematis yang mencapai 48,72% pada siklus I meningkat menjadi 61,815% pada siklus II. Rata-rata kelas pada siklus I yang semula 69,04% menjadi 87,68% pada siklus II. Serta ketuntasan klasikal mencapai 68% pada siklus I meningkat menjadi 84% pada siklus II. Sehingga dapat dikatakan bahwa penelitian selama siklus I dan siklus II menunjukkan adanya peningkatan disposisi matematis siswa dan prestasi belajar matematika dengan pembelajaran kooperatif tipe AIR.
IMPLEMENTASI PROGRAM ADIWIYATA DALAM PEMBENTUKAN KARAKTER PEDULI LINGKUNGAN DI SD MUHAMMADIYAH BODON KOTAGEDE
Authors: Riyanti Endah , Maryani Ika 
Published: February 2020

ABSTRACT This study aims to determine the planning, implementation, and evaluation of the adiwiyata program in shaping the character of caring for the environment and to find out supporting factors and obstacles in the implementation of the adiwiyata program in shaping the character of the care for the environment in SD Muhammadiyah Bodon Kotagede. This type of research is a qualitative descriptive study. Data collection methods are done through interviews, observation, and documentation. Research subjects were the principal, the adiwiyata team, teachers, and students. The validity of the data uses triangulation techniques. Analysis techniques using data collections, data reduction, data presentation and drawing conclusions. The results showed that the implementation of the adiwiyata program in shaping the character of caring for the environment had been integrated in policies that were environmentally friendly and integrated in each subject. The integration was socialized to all school members to create an environmentally friendly school agreement. The supporting factors for the implementation of the adiwiyata program are the beautiful school environment, good cooperation between the schools, adequate budget, and environmentally friendly supporting facilities that support the implementation of the adiwiyata program. Factors inhibiting the implementation of the adiwiyata program include that there are still students who are not yet aware of understanding the concept of being environmentally minded and still lacking land for the process of growing green plants.
PERAN SPIRITUALITAS TERHADAP KEMATANGAN KARIR PADA MAHASISWA UNIVERSITAS SEBELAS MARET SURAKARTA
Authors: Nurhayati Niken Fatimah 
Published: February 2020

Abstrak. Penelitian ini bertujuan untuk mendapatkan bukti empiris tentangÂ peran spritualitas terhadap kematangan karir pada mahasiswa UKM Olahraga UNS. Metode yang digunakan dalam pemilihan subjekÂ proportional cluster sampling. Didapatkan subjek sejumlah 194 mahasiswa UKM Olahraga UNS.Â Pengukuran dilakukan dengan Skala Spiritual (Cronbachâ€™s Î± 0,864) dan Skala Kematangan karirÂ (Cronbachâ€™s Î± 0,833).Â Hasil analisis data menggunakan regresi sederhana yang mendapatkan besaran sumbangan efektif spiritualitas terhadap kematangan karir sebesar 27,6%. Besaran nilai koefisien korelasi rxy = 0.525 dengan p < 0.05Â menunjukkan adanya hubungan positif spiritual dengan kematangan karir.Â Â Semakin tinggi spiritualitas, semakin tinggi kematangan karir mahasiswa UKM Olahraga UNS.Kata Kunci: Kematangan karir, Â mahasiswa, spiritualitas,UKM Olahraga UNS
Geometrical optics approximation for plane-wave scattering by a rectangular groove on a surface
Authors: Cao Zhaolou , Cui Fenping , Xian Fenglin , Li Jinhua , Pei Shixin 
Published: February 2020

Rigorous solution of plane-wave scattering by a groove based on electromagnetic theory will be time-consuming if the groove width is much larger than the illumination wavelength. To accelerate the computation, an approach based on geometrical optics approximation is developed here. The incident beam is split into several parts during reflection and refraction. Contribution of every part is superposed to obtain the electric field at the interface between the groove and air, with which diffraction theory is utilized to calculate the far-field scattered light. Results demonstrate that the approach is capable of accurately calculating plane-wave scattering by rectangular grooves with large widths in a time-efficient manner, which can be beneficial for further inverse scattering problems.
A continued method performance monitoring approach for the determination of pediatric renin samples – application within a European clinical trial
Authors: Feickert Martin , Burdman Ilja , Makowski Nina , Ali Mohsin , Bartel Anke , Burckhardt Bjoern B. 
Published: February 2020

Abstract

Background
Plasma renin levels were determined in the academia-driven, EU-funded “Labeling of Enalapril from Neonates up to Adolescents” (LENA) project to evaluate its role in pediatric heart failure. Quality-controlled bioanalysis is crucial to ensure reliable data generation. However, a comprehensive bioanalytical quality control (QC) concept to monitor the method performance within an academic environment was lacking.

Methods
Thus, a QC concept was designed encompassing regulatory guidance, international recommendations and current scientific discussions. The concept included (1) a system-suitability test, (2) verification of single bioanalytical runs by calibration curve performance and evaluation of QCs, (3) assessment of the inter-run accuracy according to Clinical Laboratory Standards Institute (CLSI) guideline, (4) monitoring of reproducibility by pediatric incurred samples, (5) blank-sample analysis and (6) participation in interlaboratory testing.

Results
The concept was successfully applied to the academic project. About 11% of single runs were identified as invalid and triggered a re-analysis of unknown samples being included in those runs. The usefulness of the customized inter-run monitoring was demonstrated and proved the good accuracy from the first to the last run. All 147 reanalyzed incurred sample pairs complied with regulatory requirements.

Conclusions
The regulatory complied QC concept was customized for the demands of academia-driven pediatric trials and contributed to the reliable quantification of 965 pediatric renin samples.
Anti-doping: Two Scientists’ Points of View
Authors: Cowan David A , Abbate Vincenzo 
Published: February 2020

Abstract
As we get close to the start of the Olympic and Paralympic Games taking place next summer in Tokyo, Japan, athletes are preparing for selection by their host nation. This preparation, like most activities, is governed by the rules of sport. One of the most important rules relates to doping, a practice that is prohibited.
Bürgerkonferenzen als Potential für einen Neuanfang der EU
Authors: Landfried Christine 
Published: February 2020

Zusammenfassung
Es ist die Hypothese des Beitrages, dass die Kluft zwischen geringer demokratischer Mitwirkung und weitreichenden politischen Kompetenzen der EU den Mangel an kulturellen Voraussetzungen der europäischen Demokratie erklärt. Zu diesen Voraussetzungen gehören Vertrauen in die europäischen Eliten und Institutionen, ein Zugehörigkeitsgefühl und die Anerkennung von Anderssein. Zunächst werden empirische Befunde zur Partizipation in der EU beschrieben und mit den Mechanismen des europäischen Regierens erklärt. Auf dieser Basis wird der konkrete Vorschlag entwickelt, die Bürger bei einem neuen Konvent zur Zukunft Europas von Anfang an wirksam zu beteiligen.
Early Prediction of University Dropouts – A Random Forest Approach
Authors: Behr Andreas , Giese Marco , Teguim K Herve D. , Theune Katja 
Published: February 2020

AbstractWe predict university dropout using random forests based on conditional inference trees and on a broad German data set covering a wide range of aspects of student life and study courses. We model the dropout decision as a binary classification (graduate or dropout) and focus on very early prediction of student dropout by stepwise modeling students’ transition from school (pre-study) over the study-decision phase (decision phase) to the first semesters at university (early study phase). We evaluate how predictive performance changes over the three models, and observe a substantially increased performance when including variables from the first study experiences, resulting in an AUC (area under the curve) of 0.86. Important predictors are the final grade at secondary school, and also determinants associated with student satisfaction and their subjective academic self-concept and self-assessment. A direct outcome of this research is the provision of information to universities wishing to implement early warning systems and more personalized counseling services to support students at risk of dropping out during an early stage of study.
Identification of two novel variants in GAA underlying infantile-onset Pompe disease in two Pakistani families
Authors: Ullah Aman , Zubaida Bibi , Cheema Huma Arshad , Naeem Muhammad 
Published: February 2020

AbstractBackgroundPompe disease (PD) is an autosomal recessive metabolic myopathy with an average incidence of one in 40,000 live births. It has a variable age of onset and can be diagnosed within the first 3 months. Heart involvement and muscle weakness are its primary manifestations.Case presentationWe describe two families affected by PD with two rare, novel variants. To date, pathogenic variants in acid α-glucosidase (GAA) alone have accounted for all cases of the disease. Both families were screened for pathogenic sequence variations. This study presents the implications of regulatory or modifier sequences in the disease pathogenesis for the first time. A homozygous missense p.Arg854Gln variant in family A and a single heterozygous variant (p.Asn925His) in family B were found to be segregating according to the disease phenotype. The variants were not detected in our in-house database comprising 50 whole-exome sequences of healthy individuals from a local unrelated Pakistani population. In silico analyses predicted that the variants would have deleterious effects on the protein structure.ConclusionsThe variants likely underlie the infantile-onset PD (IOPD) in these Pakistani families. The study expands the mutation spectrum of GAA associated with IOPD and highlights the insufficiency of screening the GAA coding sequence to determine the cause of IOPD. The work should be helpful in carrier identification, improving genetic counselling, and prenatal diagnosis.
Cardiac biomarkers by point-of-care testing – back to the future?
Authors: Collinson Paul 
Published: February 2020

Abstract
The measurement of the cardiac troponins (cTn), cardiac troponin T (cTnT) and cardiac troponin I (cTnI) are integral to the management of patients with suspected acute coronary syndromes (ACS). Patients without clear electrocardiographic evidence of myocardial infarction require measurement of cTnT or cTnI. It therefore follows that a rapid turnaround time (TAT) combined with the immediacy of results return which is achieved by point-of-care testing (POCT) offers a substantial clinical benefit. Rapid results return plus immediate decision-making should translate into improved patient flow and improved therapeutic decision-making. The development of high sensitivity troponin assays offer significant clinical advantages. Diagnostic algorithms have been devised utilising very low cut-offs at first presentation and rapid sequential measurements based on admission and 3 h sampling, most recently with admission and 1 h sampling. Such troponin algorithms would be even more ideally suited to point-of-care testing as the TAT achieved by the diagnostic laboratory of typically 60 min corresponds to the sampling interval required by the clinician using the algorithm. However, the limits of detection and analytical imprecision required to utilise these algorithms is not yet met by any easy-to-use POCT systems.
Tellurene-based saturable absorber to demonstrate large-energy dissipative soliton and noise-like pulse generations
Authors: Xu Nannan , Ma Pengfei , Fu Shenggui , Shang Xinxin , Jiang Shouzhen , Wang Shuyun , Li Dengwang , Zhang Huanian 
Published: February 2020

Abstract
Two-dimensional layered monoelemental materials (Xenes) with excellent optoelectronic properties have various property-related applications, such as energy, biomedicine, and optoelectronic devices. Xenes also show excellent performance in acting as saturable absorbers (SAs) for obtaining ultrafast laser operations. Few-layer tellurene as a typical Xenens exhibits distinct optoelectronic properties and promising practical application potential, and its nonlinear optical absorption characteristics and related ultrafast modulation applications have been investigated preliminarily. However, tellurene-based SAs to demonstrate large-energy mode-locked operations, which have special applications in industrial and scientific research areas, are seldom studied. In this work, we focus on the preparation of tellurene-based SAs and explore its applications in demonstrating large-energy mode-locked operations [dissipative soliton (DS) and noise-like pulses (NLP)]. For DS operation, the maximum average output power, pulse width, and largest pulse energy are 23.61 mW, 5.87 ps, and 1.94 nJ, respectively. NLP operation with a recorded average output power of 106.6 mW and a pulse energy of 8.76 nJ is also generated, which shows significant enhancement in comparison to previously reported Xenes-based works. Our contribution reveals the great potential and capacity of tellurene-based SAs in obtaining large-energy pulse operations and further promotes the explorative investigation of Xenes-based optoelectronic devices.
Crystal structure of catena-poly[diaqua-(μ2-oxalyl dihydrazide-κ4
N,O:N′,O′)-bis(μ2-pyridine-2,3-dicarboxylato-κ3
N,O,O′)dicadmium(II)] hexahydrate, C16H28O18N6Cd2
Authors: Zheng Xinging , Li Li , Ran Jingwen 
Published: February 2020

Abstract
C16H28O18N6Cd2, triclinic, P1̄ (no. 2), a = 7.8375(3) Å, b = 7.8877(4) Å, c = 12.0841(6) Å, α = 85.956(2)°, β = 89.833(2)°, γ = 68.269(1)°, V = 692.00(6) Å3, Z = 2, R
gt(F) = 0.0159, wR
ref(F
2) = 0.0395, T = 293(2) K.
Crystal structure of dichlorido-bis((E)-2-((pyridin-4-ylmethylene)amino)phenol)zinc(II), C24H20Cl2N4O2Zn
Authors: Adeleke Adesola A. , Zamisa Sizwe J. , Omondi Bernard 
Published: February 2020

Abstract
C24H20Cl2N4O2Zn, triclinic, P1̄ (no. 2), a = 9.9265(6) Å, b = 15.368(1) Å, c = 16.636(1) Å, α = 102.760(1)°, β = 90.385(2)°, γ = 94.112(3)°, V = 2311.4(3) Å3, Z = 4, R
gt(F) = 0.0260, wR
ref(F
2) = 0.0653, T = 100(2) K.
Crystal structure of 7-ethoxyl-6,8-difluoro-4-oxo-1-phenyl-1,4-dihydro-quinoline-3-carboxylic acid, C18H13F2N1O4
Authors: Huang Jian-Xiong , Huang Cui-Xin , Huang Guo-Ping , Xiong Yuan-Zhen , Huang Jian-Ping 
Published: February 2020

Abstract
C18H13F2NO4, triclinic, P1̄ (no. 2), a = 7.9002(13) Å, b = 9.9371(16) Å, c = 10.6852(17) Å, α = 101.390(2)°, β = 93.169(2)°, γ = 104.901(2)°, V = 789.7(2) Å3, Z = 2, R
gt(F) = 0.0567, wR
ref(F
2) = 0.1223, T = 296(2) K.
Role of GluA3 AMPA Receptor Subunits in the Presynaptic and Postsynaptic Maturation of Synaptic Transmission and Plasticity of Endbulb−Bushy Cell Synapses in the Cochlear Nucleus
Authors: Antunes Flora M. , Rubio Maria E. , Kandler Karl 
Published: February 2020

The AMPA receptor (AMPAR) subunit GluA3 has been suggested to shape synaptic transmission and activity-dependent plasticity in endbulb-bushy cell synapses (endbulb synapses) in the anteroventral cochlear nucleus, yet the specific roles of GluA3 in the synaptic transmission at endbulb synapses remains unexplored. Here, we compared WT and GluA3 KO mice of both sexes and identified several important roles of GluA3 in the maturation of synaptic transmission and short-term plasticity in endbulb synapses. We show that GluA3 largely determines the ultrafast kinetics of endbulb synapses glutamatergic currents by promoting the insertion of postsynaptic AMPARs that contain fast desensitizing flop subunits. In addition, GluA3 is also required for the normal function, structure, and development of the presynaptic terminal which leads to altered short term-depression in GluA3 KO mice. The presence of GluA3 reduces and slows synaptic depression, which is achieved by lowering the probability of vesicle release, promoting efficient vesicle replenishment, and increasing the readily releasable pool of synaptic vesicles. Surprisingly, GluA3 also makes the speed of synaptic depression rate-invariant. We propose that the slower and rate-invariant speed of depression allows an initial response window that still contains presynaptic firing rate information before the synapse is depressed. Because this response window is rate-invariant, GluA3 extends the range of presynaptic firing rates over which rate information in bushy cells can be preserved. This novel role of GluA3 may be important to allowing the postsynaptic targets of spherical bushy cells in mice use rate information for encoding sound intensity and sound localization.SIGNIFICANCE STATEMENTWe report novel roles of the glutamate receptor subunit GluA3 in synaptic transmission in synapses between auditory nerve fibers and spherical bushy cells (BCs) in the cochlear nucleus. We show that GluA3 contributes to the generation of ultrafast glutamatergic currents at these synapses, which is important to preserve temporal information about the sound. Furthermore, we demonstrate that GluA3 contributes to the normal function and development of the presynaptic terminal, whose properties shape short-term plasticity. GluA3 slows and attenuates synaptic depression, and makes it less dependent on the presynaptic firing rates. This may help BCs to transfer information about the high rates of activity that occur at the synapsein vivoto postsynaptic targets that use rate information for sound localization.
Clinico–pathological features, treatments and survival of malignant insulinomas: a multicenter study
Authors: Veltroni A , Cosaro E , Spada F , Fazio N , Faggiano A , Colao A , Pusceddu S , Zatelli M C , Campana D , Piovesan A , Pia A , Grossrubatscher E M , Filice A , Bianchi A , Razzore P , Toaiari M , Cingarlini S , Landoni L , Micciolo R , Davì M V 
Published: February 2020

Introduction
Management of malignant insulinomas is challenging due to the need to control both hypoglycaemic syndrome and tumor growth. Literature data is limited to small series.

Aim of the study
To analyze clinico-pathological characteristics, treatments and prognosis of patients with malignant insulinoma.

Materials and methods
Multicenter retrospective study on 31 patients (male: 61.3%) diagnosed between 1988 and 2017.

Results
The mean age at diagnosis was 48 years. The mean NET diameter was 41 ± 31 mm, and 70.8% of NETs were G2. Metastases were widespread in 38.7%, hepatic in 41.9% and only lymph nodal in 19.4%. In 16.1% of the cases, the hypoglycaemic syndrome occurred after 46 ± 35 months from the diagnosis of originally non-functioning NET, whereas in 83.9% of the cases it led to the diagnosis of NET, of which 42.3% with a mean diagnostic delay of 32.7 ± 39.8 months. Surgical treatment was performed in 67.7% of the cases. The 5-year survival rate was 62%. Overall survival was significantly higher in patients with Ki-67 ≤10% (P = 0.03), insulin level <60 µU/mL (P = 0.015) and in patients who underwent surgery (P = 0.006). Peptide Receptor Radionuclide Therapy (PRRT) was performed in 45.1%, with syndrome control in 93% of patients.

Conclusions
Our study includes the largest series of patients with malignant insulinoma reported to date. The hypoglycaemic syndrome may occur after years in initially non-functioning NETs or be misunderstood with delayed diagnosis of NETs. Surgical treatment and Ki67 ≤10% are prognostic factors associated with better survival. PPRT proved to be effective in the control of hypoglycaemia in majority of cases.
Genetic Analysis and Fine Mapping of a Spontaneously Mutated Male Sterility Gene inBrassica rapassp.chinensis
Authors: Lin Tzu-Kai , Lin Ya-Ping , Lin Shun-Fu 
Published: February 2020

AbstractMale sterility has been widely used in hybrid seed production in Brassica, but not in B. rapa ssp. chinensis, and genetic models of male sterility for this subspecies are unclear. We discovered a spontaneous mutant in B. rapa ssp. chinensis. A series of progeny tests indicated that male sterility in B. rapa ssp. chinensis follows a three-allele model with BrMsa, BrMsb, and BrMsc. The male sterility locus has been mapped to chromosome A07 in BC1 and F2 populations through genotyping by sequencing. Fine mapping in a total of 1,590 F2 plants narrowed the male sterility gene BrMs to a 400 kb region, with two SNP markers only 0.3 cM from the gene. Comparative gene mapping shows that the Ms gene in B. rapa ssp. pekinensis is different from the BrMs gene of B. rapa ssp. chinensis, despite that both genes are located on chromosome A07. Interestingly, the DNA sequence orthologous to a male sterile gene in Brassica napus, BnRf, is within 400 kb of the BrMs locus. The BnRf orthologs of B. rapa ssp. chinensis were sequenced, and one KASP marker (BrMs_indel) was developed for genotyping based on a 14 bp indel at intron 4. Cosegregation of male sterility and BrMs_indel genotypes in the F2 population indicated that BnRf from B. napus and BrMs from B. rapa are likely to be orthologs. The BrMs_indel marker developed in this study will be useful in marker-assisted selection for the male sterility trait.