Miracle-dz/UniFAR-FTUs huggingface dataset:
Associations Between Patient Health Outcomes and Secure Message Content Exchanged Between Patients and Clinicians: Retrospective Cohort Study

Background The number of electronic messages securely exchanged between clinic staff and patients has risen dramatically over the last decade. A variety of studies explored whether the volume of messages sent by patients was associated with outcomes. None of these studies, however, examined whether message content itself was associated with outcomes. Because secure messaging is a significant form of communication between patients and clinic staff, it is critical to evaluate the context of the communication to best understand its impact on patient health outcomes. Objective To examine associations between patients’ and clinicians’ message content and changes in patients’ health outcomes. Methods We applied a taxonomy developed specifically for secure messages to 14,394 patient- and clinic staff–generated messages derived from patient-initiated message threads. Our study population included 1602 patients, 50.94% (n=816) of whom initiated message threads. We conducted linear regression analyses to determine whether message codes were associated with changes in glycemic (A1C) levels in patients with diabetes and changes in systolic (SBP) and diastolic (DBP) blood pressure in patients with hypertension. Results Patients who initiated threads had larger declines in A1Cs (P=.01) compared to patients who did not initiate threads. Clinic nonresponse was associated with decreased SBP (β=–.30; 95% CI –0.56 to –0.04), as were staffs’ action responses (β=–30; 95% CI –0.58 to –0.02). Increased DBP, SBP, and A1C levels were associated with patient-generated appreciation and praise messages and staff encouragement with effect sizes ranging from 0.51 (A1C) to 5.80 (SBP). We found improvements in SBP associated with patients’ complaints (β=–4.03; 95% CI –7.94 to –0.12). Deferred information sharing by clinic staff was associated with increased SBP (β=1.29; 95% CI 0.4 to 2.19). Conclusions This is the first research to find associations between message content and patients’ health outcomes. Our findings indicate mixed associations between patient message content and patient outcomes. Further research is needed to understand the implications of this work; in the meantime, health care providers should be aware that their message content may influence patient health outcomes.
An update on cyclodextrins as drug vehicles for antimicrobial applications

Cyclodextrins belong to cyclic oligosaccharides comprised of α-(1,4) linked glucopyranose groups. Their interesting supramolecular cavity-like structure can host active molecules providing a breeding ground for drug delivery systems. Cyclodextrins, due to their unique functional structure, can produce host-guest complexes with active ingredients, such as drugs, peptides, proteins, etc.; the complexes resulted from intramolecular interactions leading to stable molecules vehicles. Moreover, cyclodextrins are already applied in pharmaceutical industry applications since they can induce the solubility of lipophilic compounds and provide bioavailability and excellent safety profile and stability. In this review, the basic background for cyclodextrins and their current applications in the antimicrobial field are discussed. Besides, the antibacterial and antifungal-applications in the pharmaceutical field attract most researchers because of microbes’ resistance. Regarding this, the most recent cyclodextrin inclusion complexes with antimicrobial and antifungal drugs are summarized in this article.
Streptococcus thermophiles DMST-H2 Promotes Recovery in Mice with Antibiotic-Associated Diarrhea

Antibiotic-associated diarrhea (AAD) is the most common side effect of antibiotics and is routinely treated with probiotics in clinical. Streptococcus thermophiles, extensively utilized for producing dairy foods, has recently been regarded as a new promising probiotic candidate. In this study, the efficacy of Streptococcus thermophiles DMST-H2 (DMST-H2) for AAD treatment in mice was investigated. DMST-H2 was isolated from Chinese traditional yogurt, proved to be non-toxic, and presented tolerance against simulated gastrointestinal conditions in vitro. Additionally, genomic analysis revealed that it possessed genes related to acid tolerance, bile salt tolerance, adhesion, oxidative stress and bacteriocin production. The animal experiment results showed that both DMST-H2 treatment and natural recovery could reduce fecal water content. Compared with spontaneous recovery, DMST-H2 accelerated the recovery of the enlarged caecum and intestinal barrier injury from AAD, and further decreased endotoxin (ET), D-lactate (D-LA) and diamine oxidase (DAO) content in serum. Moreover, pro-inflammatory cytokines (TNF-α) were reduced, while interferon-γ (IFN-γ) and anti-inflammatory cytokines (IL-10) increased after treating with DMST-H2. Furthermore, DMST-H2 better restored the structure of intestinal flora. At the phylum level, Firmicutes increased and Proteobacteria decreased. These findings indicate that DMST-H2 could promote recovery in mice with antibiotic-associated diarrhea.
Epistatic interactions shape the interplay between beneficial alleles and gain or loss of pathways in the evolution of novel metabolism

Fitness landscapes are often invoked to interpret the effects of allele substitutions and their interactions; however, evolution also includes larger changes like gene loss and acquisition. Previous work with the methylotrophic bacterium Methylorubrum extorquens AM1 identified strongly beneficial mutations in a strain evolved to utilize a novel, Foreign pathway in place of its native central metabolic pathway for growth on methanol. These mutations were consistently beneficial, regardless of the order in which they arose. Here we extend this analysis to consider loss or acquisition of metabolic pathways by examining strains relying upon either the Native pathway, or both (‘Dual’) pathways present. Unlike in the Foreign pathway context in which they evolved, these alleles were often deleterious in these alternative genetic backgrounds, following patterns that were strongly contingent on the specific pathways and other evolved alleles present. Landscapes for these alternative pathway backgrounds altered which genotypes correspond to local fitness peaks and would restrict the set of accessible evolutionary trajectories. These epistatic interactions negatively impact the probability of maintaining multiple degenerate pathways, making it more difficult for these pathways to coevolve. Together, our results highlight the uncertainty of retaining novel functions acquired via horizontal gene transfer (HGT), and that the potential for cells to either adopt novel functions or to maintain degenerate pathways together in a genome is heavily dependent upon the underlying epistatic interactions between them. Author Summary The evolution of physiology in microbes has important impacts ranging from global cycling of elements to the emergence and spread of pathogens and their resistance to antibiotics. While genetic interactions between mutations in evolving lineages of microbes have been investigated, these have not included the acquisition of novel genes on elements like plasmids, and thus how these elements interact with existing alleles. The dynamics of novel gene retention are of interest from both positive (e.g., biotechnology) and negative (e.g., antimicrobial resistance) practical impacts. We find that the patterns of interactions between evolved alleles appear substantially different, and generally much less positive, when moved into novel genetic backgrounds. Additionally, these preexisting alleles were found to have strong impacts on the ability of genotypes to maintain – and in rare cases coevolve with – novel genes and pathways. These results show that even though they evolved separately, the particular alleles in a genetic background, and importantly the physiological impacts they confer, weigh heavily on whether genes for novel metabolic processes are maintained.
Studies on the effect of exogenous amino acid application on nematodes

2 1 Index 9 1.1 Figures 9 1.2 Tables 11 1.3 Abbreviations 12 2 Introduction 18 2.1 Animal and plant model organisms 18 2.1.1 Heterodera schachtii 18 2.1.2 Caenorhabditis elegans 20 2.1.3 Arabidopsis thaliana 21 2.2 Amino acids 23 2.2.1 Characterization and classification 23 2.2.2 Chemical and physical characterization properties 24 2.3 Aa metabolism and transport of plants 26 2.3.1 Description of biosynthesis pathway 29 2.3.2 Regulation of the Aspartate Pathway 33 2.3.3 Aa transport in plants 35 2.4 Aa in nematode-hostplant interactions 37 2.4.1 Aa requirements of nematodes 37 2.4.2 The participation of aa transporters in host-nematode interactions 37 2.4.3 Influence of quantitative aa levels in host plants on nematode parasitism 39 2.5 Applied nematode control techniques 39 2.5. 1 Chemical nematode control 40 2.5. 2 Plant derived nematode control 40 2.5. 3 Biological nematode control 41 2.6 Effects of exogenously applied aa on nematodes 43 6 2.6. 1 Effects reported for methionine 43 2.6. 2 Effects reported for other aa 44 2.6. 3 Summary on aa induced effects on nematodes 45 3 Materials 46 3.1 Biological materials 46 3.2 Chemicals 47 3.3 Plastic and glassware 50 3.4 Instruments / machines 52 3.5 Purchased kits 54 3.6 Software 55 4 Methods 56 4.1 Preparation of test compound solutions 56 4.2 Experiments with C. elegans 56 4.2.1 Culture establishment and maintenance of C. elegans 57 4.2.2 Tests for effects on the activity of C. elegans 59 4.2.3 Effects on the development of C. elegans 60 4.3 Experiments with Heterodera schachtii 61 4.3.1 Maintenance and preparation 61 4.3.2 Maintenance and preparation of A. thaliana 63 4.3.3 Infection assay analyses 64 4.3.4 Activity test in solution 65 4.3.5 24h incubation of nematodes prior to inoculation 66 4.3.6 Knops’-medium supplemented with test compounds 67 4.3. 7 Detailed analysis of the infection and development of H. schachtii 69 4.3. 8 Infection assays with SALK_081563c and mto1-1 mutant lines 70 4.3. 9 Gene expression analysis by NEMATIC 72 4.3.10 Gene expression analysis by qRT-PCR 73
Pendidikan kepramukaan untuk penanaman nilai-nilai Pancasila di SMP Budi Mulia Pakisaji Kabupaten Malang

Tujuan penelitian ini adalah untuk menjelaskan secara deskriptif tentang rancangan, proses, dan esensi penanaman nilai-nilai Pancasila pada pendidikan Pramuka dengan subyek sebanyak 150 murid dan 3 pembina Pramuka di SMP Budi Mulia Kabupaten Malang. Jenis penelitian yang digunakan adalah penelitian kualitatif dengan model studi deskriptif. Analisis dan editing data menggunakan metode Miles & Huberman. Hasil penelitian menunjukkan bahwa (1) rancangan untuk program pendidikan Pramuka untuk menanamkan nilai Pancasila, membutuhkan adaptasi yang kompleks terutama untuk harmonisasi dengan kurikulum pendidikan yang sedang berjalan. (2) Pelaksanaan program pramuka pada aspek pengabdian dan pengamalan nilai gotong royong di masyarakat, masih membutuhkan pendampingan yang kuat untuk praktek dan aplikasi di masyarakat, mengingat peserta Pramuka yang masih duduk di bangku SMP. (3) Secara esensi penanaman nilai Pancasila di Pramuka, sesuai dengan pembangunan karakter dan kepribadian untuk anggota Pramuka, sehingga mampu mempererat dan memperkuat edukasi yang ada di SMP Budi Mulia Kabupaten Malang. Kendala dan pola penyelesaian permasalahan masih bersifat internal dan belum menyentuh problem solving secara sistematis dan komprehensif
Rethinking Breiman's Dilemma in Neural Networks: Phase Transitions of Margin Dynamics

Margin enlargement of training data has been an important strategy for perceptrons in machine learning for the purpose of boosting the confidence of training toward a good generalization ability. Yet Breiman (1999) shows a dilemma: a uniform improvement on margin distribution does not necessarily reduce generalization errors. In this paper, we revisit Breiman's dilemma in deep neural networks with recently proposed spectrally normalized margins from a novel perspective based on phase transitions of normalized margin distributions in training dynamics. Normalized margin distribution of a classifier of the data can be divided into two parts: low/small margins such as some negative margins for misclassified samples vs. high/large margins for high confident correctly classified samples, which often behave differently during the training process. Low margins for training and test datasets are often effectively reduced in training, along with reductions of training and test errors, whereas high margins may exhibit different dynamics, reflecting the trade-off between the expressive power of models and the complexity of data. When data complexity is comparable to the model expressiveness, high margin distributions for both training and test data undergo similar decrease-increase phase transitions during training. In such cases, one can predict the trend of generalization or test error through margin-based generalization bounds with restricted Rademacher complexities, shown in two ways in this paper with early stopping time exploiting such phase transitions. On the other hand, over-expressive models may have both low and high training margins undergoing uniform improvements with a distinct phase transition in test margin dynamics. This reconfirms the Breiman's dilemma associated with over-parameterized neural networks where margins fail to predict overfitting. Experiments are conducted with some basic convolutional networks, AlexNet, VGG-16, and ResNet-18, on several datasets, including Cifar10/100 and mini-ImageNet.
Effect of CAI Package on Achievement of Business Education Students in Small Business Management

This study aimed at finding out the “ Effect of Computer Assisted Instruction Package (CAIP) on academic achievement of business education students in Small Business Management (SBM) in North Eastern Universities of Nigeria”. Three null hypotheses were formulated, the study adopted quasi-experimental design. The population for the study comprised of 224 business education students that are offering SBM in 2018/2019 academic session. Simple random sampling technique was used in the selection of the universities where the sample size was 141 students, Simple random sampling technique was also used in selecting the experimental and control groups. Independent sample t-test and paired sample t-test was used in testing the null hypotheses at 0.05 level of significance. The findings of the study revealed among others, that there was a significant difference in the achievement of the students of business education taught SBM using CAIP compared to those taught using lecture method. It was concluded that CAIP is effective in teaching SBM for betterment of students’ academic achievement at university level.
Trend analysis of monsoon season monthly rainfall of Nagwan watershed

The daily rainfall data for a period of 32 years from 1983-2014 of gauging station located in Nagwan watershed of Hazaribagh, Jharkhand were analyzed to study variation of monsoon months and monsoon season rainfall distribution pattern and its trend. The monsoon months and monsoon season rainfall series from daily data were developed. The mean, standard deviation, coefficient of variation, coefficient of skewness and kurtosis of monsoon months and monsoon season rainfall series were calculated. The percentage contributions of monthly rainfall to monsoon season rainfall values were also calculated. Frequency distributions of monsoon months and monsoon season rainfall were developed. The monsoon months and monsoon season rainfall time series were splitted in four sub-periods viz. 1983-1989, 1990-1999, 2000-2009 and 2010-2014. The difference in mean of monsoon months and monsoon season rainfall were tested by student t-test at 5% level of significance. The trend in monthly and monsoon season rainfall were tested by Mann-Kendall rank correlation test, Sen's slope estimator method and by regression test for linear trend. The value of Mann-Kendall statistic is negative for June, July, August, September and Monsoon season rainfall indicating a falling trend. However trend is not significant in all the cases at 5% significance level. Rising trend for the month of August and falling trend in case of June, July, September and Monsoon season are observed by Sen’s method. No significant rising or falling trend on the regression slope for all the time series is observed at 5% level of significance.
Sequence analysis orfipy: a fast and flexible tool for extracting ORFs

Summary: Searching for open reading frames is a routine task and a critical step prior to annotating protein coding regions in newly sequenced genomes or de novo transcriptome assemblies. With the tremendous increase in genomic and transcriptomic data, faster tools are needed to handle large input datasets. These tools should be versatile enough to ﬁne-tune search criteria and allow efﬁcient downstream analysis. Here we present a new python based tool, orﬁpy, which allows the user to ﬂexibly search for open reading frames in genomic and transcriptomic sequences. The search is rapid and is fully customizable, with a choice of FASTA and BED output formats. Availability and implementation: orﬁpy is implemented in python and is compatible with python v3.6 and higher. Source code: https://github.com/urmi-21/orﬁpy. Installation: from the source, or via PyPi (https://pypi.org/project/ orﬁpy) or bioconda (https://anaconda.org/bioconda/orﬁpy).
Fuzzy LDA for Topic Modeling: An Overview

Topic modeling is underway from text-mining as well as data mining techniques for determining the suppressed semantic assembly in a collection of various dataset. In the conception of text mining every document is engendered from gathering of topics. Subject modeling is constructed on probabilistic modeling, it has a enormous, variety of solicitations such as morphological sympathetic, image detection, involuntary music creativeness identification etc. Topic modeling is implemented in many grounds such as software engineering development, civil engineering, bio medical environment etc. We describe a topic modeling using fuzzy LDA (Latent Dirichelt Allocation). Basically fuzzy logic algorithm generates the probability for LDA which cultivates the classification accuracy of structured as well as semi structured data. The system illustrates topic modeling on synthetic as well as real time data and evaluates the extensive performance analysis with various parameter tuning methods.
Candidate Gene Analysis Reveals Strong Association of CETP Variants With High Density Lipoprotein Cholesterol and PCSK9 Variants With Low Density Lipoprotein Cholesterol in Ghanaian Adults: An AWI-Gen Sub-Study

Variations in lipid levels are attributed partly to genetic factors. Genome-wide association studies (GWASs) mainly performed in European, African American and Asian cohorts have identified variants associated with LDL-C, HDL-C, total cholesterol (TC) and triglycerides (TG), but few studies have been performed in sub-Saharan Africans. This study evaluated the effect of single nucleotide variants (SNVs) in eight candidate loci (ABCA1, LCAT, LPL, PON1, CETP, PCSK9, MVK, and MMAB) on lipid levels among 1855 Ghanaian adults. All lipid levels were measured directly using an automated analyser. DNA was extracted and genotyped using the H3Africa SNV array. Linear regression models were used to test the association between SNVs and log-transformed lipid levels, adjusting for sex, age and waist circumference. In addition Bonferroni correction was performed to account for multiple testing. Several variants of CETP, LCAT, PCSK9, and PON1 (MAF > 0.05) were associated with HDL-C, LDL-C and TC levels at p < 0.05. The lead variants for association with HDL-C were rs17231520 in CETP (β = 0.139, p < 0.0001) and rs1109166 in LCAT (β = −0.044, p = 0.028). Lower LDL-C levels were associated with an intronic variant in PCSK9 (rs11806638 [β = −0.055, p = 0.027]) and increased TC was associated with a variant in PON1 (rs854558 [β = 0.040, p = 0.020]). In silico functional analyses indicated that these variants likely influence gene function through their effect on gene transcription. We replicated a strong association between CETP variants and HDL-C and between PCSK9 variant and LDL-C in West Africans, with two potentially functional variants and identified three novel variants in linkage disequilibrium in PON1 which were associated with increasing TC levels in Ghanaians.
Factors influencing the willingness-to-pay of internet users in Vietnam for the fee-based online contents

The aim of this study is to identify key factors that influence the willingness-to-pay (WTP) of Internet users in Vietnam for fee-based online contents. The study collects 309 suitable questionnaires filled by internet users over 18 years old and living in Vietnam, who frequently use online contents and have ideally made payment for online contents. The analysis results indicate that the willingness-to-pay for the fee-based online contents of Vietnamese users are influenced by their attitudes toward paying and ethical self-efficacy for online piracy. The study also identifies the antecedents of attitude, which include the perceived benefits of usefulness and enjoyment, the perceived sacrifice of the fee, social influences from other people, and especially the free mentality. The study then suggests managerial implications to online content providers in enhancing WTP for the fee-based online contents in Vietnam.
Comparing the foraging behaviour and pollination efficiency of Apis mellifera with Xylocopa olivacea (Apidae: Hymenoptera) on Citrullus lanatus flowers

Comparing the foraging behaviour and the pollination efficiency of honey bee (Apis mellifera) with a carpenter bee (Xylocopa olivacea) in the farmer garden of watermelon (Citrullus lanatus) was conducted in Maroua (Cameroun) in 2016 and 2017. Several foraging parameters were assessed for each bee species during the blooming period of watermelon and comparisons were made between fruit and seed yields from four pollination treatments on female flowers including the no bee visit treatment (T0), the one bee visit treatment for A. mellifera (T1) and X. olivacea (T2) and the unrestricted treatment (T3). Results showed an important difference in the rhythm of activity between the two bee species with a peak of floral activity of X. olivacea at 07:00-08:00 a.m. time interval and that of A. mellifera at 09:00-10:00 a.m. A. mellifera was prominent than X. olivacea regarding the frequency of floral visits in 2016 (77.74 and 22.26 %) and in 2017 (81.28 and 18.72 %) and the density of individuals per 1000 flowers in 2016 (442/1000 flowers and 97/1000 flowers) and in 2017 (476/1000 flowers and 88/1000 flowers). Despite the higher foraging intensity of A. mellifera compared with that of X. olivacea, the carpenter bee was a more efficient pollinator than the honey bee. Indeed, the mean treatments for fruiting rate, mean fruit weight, mean fruit diameter, and mean mature seeds per fruit of watermelon were higher on the one visit basis in T2 than T1. Moreover, the unrestricted treatment T3 produced fruit with the best marketable value than restricted treatments T2, T1, and T0. X. olivacea should be associated with A. mellifera in a watermelon field to optimize the pollination of this crop for obtaining improved yields. Considering very high pollinating efficiency of X. olivacea, the means of conservation must be developed for this solitary bee which appeared in this work as a synergistic or alternative pollinator of the honey bee within a watermelon farm.