Miracle-dz/UniFAR-FTUs huggingface dataset:
Catchment-scale export of antibiotic resistance genes and bacteria from an agricultural watershed in central Iowa

Antibiotics are administered to livestock in animal feeding operations (AFOs) for the control, prevention, and treatment of disease. Manure from antibiotic treated livestock contains unmetabolized antibiotics that provide selective pressure on bacteria, facilitating the expression of anti-microbial resistance (AMR). Manure application on row crops is an agronomic practice used by growers to meet crop nutrient needs; however, it can be a source of AMR to the soil and water environment. This study in central Iowa aims to directly compare AMR indicators in outlet runoff from two adjacent (221 to 229 ha) manured and non-manured catchments (manure comparison), and among three catchments (600 to 804 ha) with manure influence, no known manure application (control), and urban influences (mixed land use comparison). Monitored AMR indicators included antibiotic resistance genes (ARGs) ermB, ermF (macrolide), tetA, tetM, tetO, tetW (tetracycline), sul1, sul2 (sulfonamide), aadA2 (aminoglycoside), vgaA, and vgaB (pleuromutilin), and tylosin and tetracycline resistant enterococci bacteria. Results of the manure comparison showed significantly higher (p<0.05) tetracycline and tylosin resistant bacteria from the catchment with manure application in 2017, but no differences in 2018, possibly due to changes in antibiotic use resulting from the Veterinary Feed Directive. Moreover, the ARG analysis indicated a larger diversity of ARGs at the manure amended catchment. The mixed land use comparison showed the manure amended catchment had significantly higher (p<0.05) tetracycline resistant bacteria in 2017 and significantly higher tylosin resistant bacteria in 2017 and 2018 than the urban influenced catchment. The urban influenced catchment had significantly higher ermB concentrations in both sampling years, however the manure applied catchment runoff consisted of higher relative abundance of total ARGs. Additionally, both catchments showed higher AMR indicators compared to the control catchment. This study identifies four ARGs that might be specific to AMR as a result of agricultural sources (tetM, tetW, sul1, sul2) and optimal for use in watershed scale monitoring studies for tracking resistance in the environment.
Uncoupling sodium channel dimers rescues phenotype of pain-linked Nav1.7 mutation

The voltage-gated sodium channel Nav1.7 is essential for an adequate perception of painful stimuli. Its mutations cause various pain syndromes in human patients. The hNav1.7/A1632E mutation induces symptoms of erythromelalgia and paroxysmal extreme pain disorder (PEPD), and its main gating change is a strongly enhanced persistent current. Using molecular simulations, we demonstrate that the disease causing persistent current of hNav1.7/A1632E is due to impaired binding of the IFM motif, thus affecting proper function of the recently proposed allosteric fast inactivation mechanism. By using native polyacrylamide gel electrophoresis (PAGE) gels, we show that hNav1.7 dimerizes. The disease-linked persistent current depends on the channel’s functional dimerization status: Using difopein, a 14-3-3 inhibitor known to uncouple dimerization of hNav1.5, we detect a significant decrease in hNav1.7/A1632E induced persistent currents. Our work identifies that functional uncoupling of hNav1.7/A1632E dimers rescues the pain-causing molecular phenotype by interferes with an allosteric fast inactivation mechanism, which we link for the first time to channel dimerization. Our work supports the concept of sodium channel dimerization and reveals its relevance to human pain syndromes.
A Project-Based Biology Unit: Star Athlete Collapses on the Football Field

Abstract Students in a high school biology class were introduced to the case of “Marcus” (a pseudonym), a high school football player who collapsed on the football field during a game and was rushed to the emergency room with various symptoms. Throughout the two-week, project-based unit, students worked in cooperative groups to diagnose Marcus, learning about various inherited diseases and heat-related ailments that might impact young athletes. This unit integrates ultrasound technology into the classroom as a teaching and diagnostic technique and introduces students to health science careers. Student groups work to produce a final product that is presented to a public audience (e.g., parents, teachers, coaches) to increase their awareness of the science content underlying the causes of sudden collapses in young athletes. This learning experience ended with students individually writing a letter to Marcus's family explaining his diagnosis and the related biology concepts.
Effect of a rapid heat treatment on Thai QX-like infectious bronchitis virus and evaluation of protection induced by a heat-treated virus

The purpose of this study was to evaluate the effect of a rapid heat-treatment method on Thai QX-like infectious bronchitis virus (IBV) and the efficacy on protection from the virus after heat treatment. QX-like IBV isolate THA46 was incubated at 56 o C. The incubated virus was collected every 5 min for up to 1 h and then they were inoculated into embryonated chicken eggs. At 6 days post-inoculation, allantoic fluid was harvested from the embryonated eggs which were inoculated with virus of the longest heat-treatment time that induced lesions in the embryos. That allantoic fluid was used in a subsequent round of heat treatment followed by inoculation into embryonated eggs. The procedure was repeated eight times. The longest heat-treatment time at 56 o C that induced lesions in the embryos for Thai QX-like IBV varied from 30 to 60 min. S1 and N genes of the virus after each heat-treatment time were sequenced and none of the nucleotide changes were found. The efficacy of the heat-treated virus was investigated by immunizing chicks at 1 and 14 days of age and challenging with the pathogenic isolate THA46 at 28 days of age. The results showed that virus detection in the tracheas, the gross lesion score of the tracheas and the histopathologic lesion score of the tracheas and kidneys of the chickens immunized with heat-treated virus were significantly lower ( p <0.05) than those of the positive control group. The study demonstrates that a rapid heat-treatment method has no effect on the S1 and N gene of IBV isolate used in this work. A heat-treated Thai QX-like IBV provided a good protection against challenge with pathogenic Thai QX-like IBV.
The Gene Expression Deconvolution Interactive Tool (GEDIT): accurate cell type quantification from gene expression data

The cell type composition of heterogeneous tissue samples can be a critical variable in both clinical and laboratory settings. However, current experimental methods of cell type quantification (e.g. cell flow cytometry) are costly, time consuming, and can introduce bias. Computational approaches that infer cell type abundance from expression data offer an alternate solution. While these methods have gained popularity, most are limited to predicting hematopoietic cell types and do not produce accurate predictions for stromal cell types. Many of these methods are also limited to particular platforms, whether RNA-seq or specific microarrays. We present the Gene Expression Deconvolution Interactive Tool (GEDIT), a tool that overcomes these limitations, compares favorably with existing methods, and provides superior versatility. Using both simulated and experimental data, we extensively evaluate the performance of GEDIT and demonstrate that it returns robust results under a wide variety of conditions. These conditions include a variety of platforms (microarray and RNA-seq), tissue types (blood and stromal), and species (human and mouse). Finally, we provide reference data from eight sources spanning a wide variety of stromal and hematopoietic types in both human and mouse. This reference database allows the user to obtain estimates for a wide variety of tissue samples without having to provide their own data. GEDIT also accepts user submitted reference data, thus allowing the estimation of any cell type or subtype, provided that reference data is available. Author Summary The Gene Expression Deconvolution Interactive Tool (GEDIT) is a robust and accurate tool that uses gene expression data to estimate cell type abundances. Extensive testing on a variety of tissue types and technological platforms demonstrates that GEDIT provides greater versatility than other cell type deconvolution tools. GEDIT utilizes reference data describing the expression profile of purified cell types, and we provide in the software package a library of reference matrices from various sources. GEDIT is also flexible and allows the user to supply custom reference matrices. A GUI interface for GEDIT is available at http://webtools.mcdb. ucla.edu/, and source code and reference matrices are available at https://github.com/BNadel/GEDIT.
Characterizing microsatellite polymorphisms using assembly-based and mapping-based tools

Microsatellite polymorphism has always been a challenge for genome assembly and sequence alignment due to sequencing errors, short read lengths, and high incidence of polymerase slippage in microsatellite regions. Despite the information they carry being very valuable, microsatellite variations have not gained enough attention to be a routine step in genome sequence analysis pipelines. After the completion of the 1000 Genomes Project, which aimed to establish the most detailed genetic variation catalog for humans, the consortium released only two microsatellite prediction sets generated by two tools. Many other large research efforts have failed to shed light on microsatellite variations. We evaluated the performance of three different local assembly methods on three different experimental settings, focusing on genotype-based performance, coverage impact, and preprocessing including flanking regions. All these experiments supported our initial expectations on assembly. We also demonstrate that overlap-layout-consensus (OLC)-basedassembly methods show higher sensitivity to microsatellite variant calling when compared to a de Bruijn graph-based approach. We conclude that assembly with OLC is the better method for genotyping microsatellites. Our pipeline is available at https://github.com/gulfemd/STRAssembly.
Simulating bipedal walking using a translating center of pressure

During walking, foot orientation and foot placement allow humans to stabilize their gait and to move forward. Consequently the upper body adapts to the ground reaction force (GRF) transmitted through the feet. The foot-ground contact is often modeled as a fixed pivot in bipedal models for analysis of locomotion. The fixed pivot models, however, cannot capture the effect of shift in the pivot point from heel to toe. In this study, we propose a novel bipedal model, called SLIPCOP, which employs a translating center of pressure (COP) in a spring loaded inverted pendulum (SLIP) model. The translating COP has two modes: one with a constant speed of translation and the other as the weighted function of the GRF in the fore aft direction. We use the relation between walking speed and touchdown (TD) angle as well as walking speed and COP speed, from existing literature, to restrict steady state solutions within the human walking domain. We find that with these relations, SLIPCOP provides steady state solutions for very slow to very fast walking speeds unlike SLIP. SLIPCOP for normal to very fast walking speed shows good accuracy in estimating COM amplitude and swing stance ratio. SLIPCOP is able to estimate the distance traveled by the COP during stance with high precision.
How Psychotherapists Handle Difficult Clients

Summary Although librarians occasionally encounter difficult patrons in the course of their work, psychologists work with difficult clients much more frequently. This raises an interesting question-how is it that psychologists are able to manage these trying individuals, and in some instances even help them improve? This study attempts to answer that question by investigating how psychotherapists define, cope with, and treat difficult patients. It explains the psychology of difficult clients, techniques psychologists useinworking with them, and how these might be utilized by librarians. The importance of seeing difficult clients as a means of personal growth is also emphasized.
Neural sequence-to-sequence models for low-resource morphology

The vocabularies of morphologically rich languages, e.g., German or Spanish, are much larger than those of morphologically poor languages, e.g., Chinese. This is due to processes like composition, inflection and derivation. A result of this is an increased number of rare words, which motivates the development of models that can deal with rare words by either analyzing or generating them. This thesis presents approaches to generate morphological inflections or analyze word forms through canonical segmentation. We employ state-of-the art deep learning models, namely encoder-decoder gated recurrent neural networks with attention. For analysis, we simply encode the input word and output the final segments as one word with segmentation markers. For generation, instead of only encoding the source form, we further encode additional information about the source and target forms: their morphological tags. This enables us to train one single model for all combinations of source and target tags. Our approach can thus be seen as multi-task learning by considering each such combination a separate task. It enables parameter sharing and strongly boosts the overall performance of our models. In theory, our methods are language independent. However, due to neural networks requiring large amounts of training data, limited availability of suitable training examples is a big challenge. In this work, we focus particularly on lowresource languages. In order to make up for missing training data, we experiment with transfer learning to leverage knowledge from related languages. We show that similar languages can improve performance of morphological generation systems in low-resource settings. Further, we investigate semi-supervised training, making use of large unlabeled corpora. Finally, we focus on the fact that in morphologically rich languages paradigms usually consist of more than one form and present solutions for such multi-source settings. We show that both our proposed approaches — a model accepting multisource input and a fine-tuning approach which is related to domain adaptation — improve generation performance.
Automatic Genetic Fuzzy c-Means

Abstract Fuzzy c-means is an efficient algorithm that is amply used for data clustering. Nonetheless, when using this algorithm, the designer faces two crucial choices: choosing the optimal number of clusters and initializing the cluster centers. The two choices have a direct impact on the clustering outcome. This paper presents an improved algorithm called automatic genetic fuzzy c-means that evolves the number of clusters and provides the initial centroids. The proposed algorithm uses a genetic algorithm with a new crossover operator, a new mutation operator, and modified tournament selection; further, it defines a new fitness function based on three cluster validity indices. Real data sets are used to demonstrate the effectiveness, in terms of quality, of the proposed algorithm.
Bee Visitation and Fruit Quality in Berries Under Protected Cropping Vary Along the Length of Polytunnels

Abstract Wild and managed bees provide effective crop pollination services worldwide. Protected cropping conditions are thought to alter the ambient environmental conditions in which pollinators forage for flowers, yet few studies have compared conditions at the edges and center of growing tunnels. We measured environmental variables (temperature, relative humidity, wind speed, white light, and UV light) and surveyed activity of the managed honey bee, Apis mellifera L. ; wild stingless bee, Tetragonula carbonaria Smith; and wild sweat bee, Homalictus urbanus Smith, along the length of 32 multiple open-ended polyethylene growing tunnels. These were spaced across 12 blocks at two commercial berry farms, in Coffs Harbour, New South Wales and Walkamin, North Queensland, Australia. Berry yield, fresh weight, and other quality metrics were recorded at discrete increments along the length of the tunnels. We found a higher abundance and greater number of flower visits by stingless bees and honey bees at the end of tunnels, and less frequent visits to flowers toward the middle of tunnels. The center of tunnels experienced higher temperatures and reduced wind speed. In raspberry, fruit shape was improved with greater pollinator abundance and was susceptible to higher temperatures. In blueberry, per plant yield and mean berry weight were positively associated with pollinator abundance and were lower at the center of tunnels than at the edge. Fruit quality (crumbliness) in raspberries was improved with a greater number of visits by sweat bees, who were not as susceptible to climatic conditions within tunnels. Understanding bee foraging behavior and changes to yield under protected cropping conditions is critical to inform the appropriate design of polytunnels, aid pollinator management within them, and increase economic gains in commercial berry crops.
PSIII-1 Nutritive value of expeller-pressed carinata cake for pigs

Carinata (Brasicca carinata) is an oilseed crop of brassica family that is grown for production of oil for biofuel industry. Expeller-pressed carinata cake (EPCAR), a co-product from carinata seed oil extraction plants, is available for livestock feeding. However, nutritive value of EPCAR for pigs has not been reported. Objective of this study was to determine standardized ileal digestibility (SID) of amino acids (AA) and net energy value of EPCAR for growing pigs. Eight ileal-cannulated barrows (initial BW = 33 kg) were fed 3 diets in a replicated 3 × 3 Latin square design with 2 added columns to give 8 replicates/diet. The diets were cornstarch-based, containing expeller-pressed canola cake (EPCAN) or EPCAR as sole protein source, and N-free. The EPCAN was included in the study for comparison because it is derived from canola, which is the most widely used crop of Brassica family for oil production. Digestibility of AA in feedstuffs was determined by the direct method. Energy digestibility in EPCAN and EPCAR was determined by difference from the N-free diet. On DM basis, EPCAN and EPCAR contained 39.6 and 50.2% CP, 20.7 and 26.8% NDF, 16.0 and 0.88% ether extract, 2.32 and 1.82% lysine, 0.74 and 0.96% methionine, 1.63 and 1.89% threonine, and 0.50 and 0.64% tryptophan, respectively. The EPCAN compared with EPCAR, had greater (PPP = 0.078) in SID of threonine. The EPCAN had greater (P < 0.05) net energy value than EPCAN (2,082 vs. 1,576 kcal/kg DM). In conclusion, EPCAR lower energy value than EPCAN. However, EPCAR had greater SID of most AA than EPCAN; therefore, EPCAR can serve as alternative oilseed co-product feedstuff for pigs.
A Galaxy-based training resource for single-cell RNA-seq quality control and analyses

Background It is not a trivial step to move from single-cell RNA-seq (scRNA-seq) data production to data analysis. There is a lack of intuitive training materials and easy-to-use analysis tools, and researchers can find it difficult to master the basics of scRNA-seq quality control and analysis. Results We have developed a range of easy-to-use scripts, together with their corresponding Galaxy wrappers, that make scRNA-seq training and analysis accessible to researchers previously daunted by the prospect of scRNA-seq analysis. The simple command-line tools and the point-and-click nature of Galaxy makes it easy to assess, visualise, and quality control scRNA-seq data. Conclusion We have developed a suite of scRNA-seq tools that can be used for both training and more in-depth analyses.
Causes and Consequences of the Dysregulated Maternal Renin-Angiotensin System in Preeclampsia

A healthy pregnancy outcome depends on the activation of the renin-angiotensin-aldosterone system (RAAS) as a regulated, integrated response to the growing demands of the conceptus. Both the circulating RAAS and the intrarenal renin-angiotensin system (iRAS) play major roles in cardiovascular function and fluid and electrolyte homeostasis. The circulating RAAS becomes dysfunctional in preeclampsia and we propose that dysregulation of the iRAS plays a role in development of the clinical syndrome known as preeclampsia. Experimental studies in animals have shown that placental renin, when released into the maternal circulation, can cause hypertension. We postulate that abnormal placental development is associated with over-secretion of renin and other RAS proteins/angiotensin (Ang) peptides by the placenta/decidua into the maternal circulation. We hypothesise that this is because of increased shedding of exosomes and other placental particles into the maternal circulation that not only contain RAS proteins and peptides but also microRNAs (miRNAs) that target RAS mRNAs, and Ang II type 1 receptor autoantibodies (AT1R-AAs), that are agonists for, and have the same actions as, Ang II. As a result, there is both suppression of the circulating RAAS that is responsible for maintaining maternal homeostasis and activation of the iRAS. Together with altered vascular reactivity to Ang peptides, the iRAS causes hypertension, renal damage and secondary changes in the neurohumoral control of the maternal circulation and fluid and electrolyte balance, which contribute to the pathophysiology of preeclampsia.
Trimester-specific Zika virus infection affects placental responses in women

Zika virus (ZIKV) infection during pregnancy is associated with neurologic birth defects, but the effects on placental development are unclear. Full-term placentas from three women, each infected with ZIKV during specific pregnancy trimesters, were harvested for anatomic, immunologic and transcriptomic analysis. In this study, each woman exhibited a unique immune response, but they collectively diverged from healthy controls with raised IL-1RA, IP-10, EGF and RANTES expression, and neutrophil numbers during the acute infection phase. Although ZIKV NS3 antigens co-localized to placental Hofbauer cells, the placentas showed no anatomical defects. Transcriptomic analysis of samples from the placentas revealed that infection during trimester 1 caused a disparate cellular response centered on differential eIF2 signaling, mitochondrial dysfunction and oxidative phosphorylation. These findings should translate to improve clinical prenatal screening procedures for virus-infected pregnant patients.
Isolation of intragenic suppressor of tsp-15-splicing mutant in Caenorhabditis elegans

Figure 1 (A) Representation of the position of the sv15 and im9 mutations in tsp-15, and the effects of the mutations on the splicing of intron 4. The sv15 mutation alters the splice donor site, and a cryptic splice donor in the middle of intron 4 is often used (Moribe et al. 2004). The intragenic im9 mutation abolishes the cryptic donor site, resulting in reuse of the original donor site and partial recovery of the wild-type transcript. (B) Design of qRT-PCR analysis using TaqMan probe for detecting correctly spliced tsp-15 transcript. The positions of primers and TaqMan MGB probe are indicated. R, reporter; NFQ, nonfluorescent quencher; MGB, minor groove binder. (C) Relative expression levels of correct tsp-15 transcripts. Data are mean RQ value and error bars indicate RQmin/RQmax (confidence set at 95%). ok881 is a null allele of tsp-15 having a deletion in the tsp-15 coding region (Moribe et al. 2012). (D) Representation of splice pattern of tsp-15 cDNA from sv15im9. Among 12 tsp-15 cDNA subclones, we found 3 correctly spliced products, 3 containing read-through of intron 4, and 6 aberrant transcripts using -GTin exon 4 as a cryptic splice donor.