Miracle-dz/UniFAR-FTUs huggingface dataset:
Analysis of Growth of Lactobacillus plantarum WCFS1 on a Complex Medium Using a Genome-scale Metabolic Model*

A genome-scale metabolic model of the lactic acid bacterium Lactobacillus plantarum WCFS1 was constructed based on genomic content and experimental data. The complete model includes 721 genes, 643 reactions, and 531 metabolites. Different stoichiometric modeling techniques were used for interpretation of complex fermentation data, as L. plantarum is adapted to nutrient-rich environments and only grows in media supplemented with vitamins and amino acids. (i) Based on experimental input and output fluxes, maximal ATP production was estimated and related to growth rate. (ii) Optimization of ATP production further identified amino acid catabolic pathways that were not previously associated with free-energy metabolism. (iii) Genome-scale elementary flux mode analysis identified 28 potential futile cycles. (iv) Flux variability analysis supplemented the elementary mode analysis in identifying parallel pathways, e.g. pathways with identical end products but different co-factor usage. Strongly increased flexibility in the metabolic network was observed when strict coupling between catabolic ATP production and anabolic consumption was relaxed. These results illustrate how a genome-scale metabolic model and associated constraint-based modeling techniques can be used to analyze the physiology of growth on a complex medium rather than a minimal salts medium. However, optimization of biomass formation using the Flux Balance Analysis approach, reported to successfully predict growth rate and by product formation in Escherichia coli and Saccharomyces cerevisiae, predicted too high biomass yields that were incompatible with the observed lactate production. The reason is that this approach assumes optimal efficiency of substrate to biomass conversion, and can therefore not predict the metabolically inefficient lactate formation.
Active Replication of Porcine Cytomegalovirus (PCMV) Following Transplantation of a Pig Heart into a Baboon despite Undetected Virus in the Donor Pig

Viral zoonoses may represent a serious problem when xenotransplantation using pig cells, tissues, and organs will be performed. Recently we reported multiorgan failure, mainly liver failure, in a baboon (Papio anubis) after orthotopic transplantation of a heart from a genetically modified pig and showed that the baboon was not infected with hepatitis E virus (HEV). Since pigs are frequently infected with porcine cytomegalovirus (PCMV), and the infection is latent and therefore difficult to detect, screening for PCMV was performed, using a highly sensitive real-time PCR and a nested PCR. In addition, to confirm the absence of HEV, more specific immunological methods and a real-time PCR were used. Only two out of six available pigs, including the selected donor animal, were found negative for both viruses. Nevertheless, PCMV was detected in the blood of the baboon. The titre of PCMV in the blood was above 3x104/ ml and analysis of its sequence confirmed that it was PCMV, but not baboon CMV. The data highlight a considerable risk of PCMV infection and call for regular screening of donor pigs applying the most sensitive detection methods.
Efficacy of adaptive directed transfer function for neural connectivity estimation of EEG signal during meditation

Electroencephalogram (EEG) is widely used in cognitive science, neuroscience and physiological research. It is a good mean to observe cognitive response that depends on time. EEG has many advantages over other techniques owing to its non-invasiveness, low cost and high temporal resolution. But one of the major challenges of EEG signal study is the huge data dimensionality which makes signal processing and subsequent analysis an uphill task. The aim of this study is to obtain a model for better neural connectivity analysis which illustrates meditation's dynamic mind-body response. Accordingly the EEG data is being collected during meditation (Kriya Yoga). In order to calculate and visualize the time-frequency representations of each electrode, a time varying Granger Causality based connectivity estimators named Directed Transfer Function (DTF) and adaptive DTF (ADTF) among all scalp electrodes have been computed in meditator group. The ADTF can be derived from the coefficients of a time-varying multivariate autoregressive (TVAR) model fitted to the data obtained during meditation. We define this time-varying measure of causality as the adaptive directed transfer function (ADTF) and compare its ability with the conventional DTF for meditator group. Both ADTF and Conventional DTF were calculated in meditator. The obtained simulation results of adaptive DTF and conventional DTF shows better neural connectivity and gives useful information in meditator group. However, to accomplish this task, surrogate data statistics has been used in both the mentioned models to validate the models. It was found that the ADTF has the capability to distinguish the dynamic changes in the primary source of the information outflow. The results obtained both by using ADTF and conventional DTF method were compared in meditator group subsequently.
Assessment of Neuromuscular Function After Different Strength Training Protocols Using Tensiomyography

Abstract De Paula Simola, RÁ, Harms, N, Raeder, C, Kellmann, M, Meyer, T, Pfeiffer, M, and Ferrauti, A. Assessment of neuromuscular function after different strength training protocols using tensiomyography. J Strength Cond Res 29(5): 1339–1348, 2015—The purpose of the study was to analyze tensiomyography (TMG) sensitivity to changes in muscle force and neuromuscular function of the muscle rectus femoris (RF) using TMG muscle properties after 5 different lower-limb strength training protocols (multiple sets; DS = drop sets; eccentric overload; FW = flywheel; PL = plyometrics). After baseline measurements, 14 male strength trained athletes completed 1 squat training protocol per week over a 5-week period in a randomized controlled order. Maximal voluntary isometric contraction (MVIC), TMG measurements of maximal radial displacement of the muscle belly (Dm), contraction time between 10 and 90% of Dm (Tc), and mean muscle contraction velocities from the beginning until 10% (V10) and 90% of Dm (V90) were analyzed up to 0.5 (post-train), 24 (post-24), and 48 hours (post-48) after the training interventions. Significant analysis of variance main effects for measurement points were found for all TMG contractile properties and MVIC (p < 0.01). Dm and V10 post-train values were significantly lower after protocols DS and FW compared with protocol PL (p = 0.032 and 0.012, respectively). Dm, V10, and V90 decrements correlated significantly to the decreases in MVIC (r = 0.64–0.67, p ⩽ 0.05). Some TMG muscle properties are sensitive to changes in muscle force, and different lower-limb strength training protocols lead to changes in neuromuscular function of RF. In addition, those protocols involving high and eccentric load and a high total time under tension may induce higher changes in TMG muscle properties.
Political Competition: How to Measure Party Strategy in Direct Voter Communication using Social Media Data?

Political competition, party strategy and communication in the era of social media are growing issues. Due to the increasing social media presence of parties and voters alike, direct communication is more important for party competition. This paper aims to improve the methodological approach used to analyze political competition and communication. The dataset includes over 30,000 Facebook status messages posted by seven German parties from January 2014 until February 2018. Topic modeling, which is commonly used in other fields, allows for evaluating party communication on a daily basis. The results show the high accuracy of calculating party-relevant issues. To determine the tone of the debate, a sentiment analysis was conducted. The prevalence of topics and sentiments over time allows for precise monitoring of the political debate.
Effect of Type 2 Diabetes Mellitus on Left Ventricular Geometry and Systolic Function in Hypertensive Subjects: Hypertension Genetic Epidemiology Network (HyperGEN) Study

Background—Type 2 diabetes is a cardiovascular risk factor. It remains to be elucidated in a large, population-based sample whether diabetes is associated with changes in left ventricular (LV) structure and systolic function independent of obesity and systolic blood pressure (BP). Methods and Results—Among 1950 hypertensive participants in the HyperGEN Study without overt coronary heart disease or significant valve disease, 20% (n=386) had diabetes. Diabetics were more likely to be women, black, older, and have higher BMI and waist/hip ratio than were nondiabetics. After adjustment for age and sex, diabetics had higher systolic BP, pulse pressure, and heart rate; lower diastolic BP; and longer duration of hypertension than nondiabetics. LV mass and relative wall thickness were higher in diabetic than nondiabetic subjects independent of covariates. Compared with nondiabetic hypertensives, diabetics had lower stress-corrected midwall shortening, independent of covariates, without difference in LV EF. Insulin levels and insulin resistance were higher in non–insulin-treated diabetics (n=195) than nondiabetic (n=1439) subjects (both P <0.01). Insulin resistance positively but weakly related to LV mass and relative wall thickness. Conclusions—In a relatively healthy, population-based sample of hypertensive adults, type 2 diabetes was associated with higher LV mass, more concentric LV geometry, and lower myocardial function, independent of age, sex, body size, and arterial BP.
The role of non-viraemic transmission on the persistence and dynamics of a tick borne virus – Louping ill in red grouse ( Lagopus lagopus scoticus ) and mountain hares ( Lepus timidus )

There exist many tick borne infections that are of either economic or public health interest. Mathematical models have previously been used to describe the dynamics of these infections. However it has recently come to light that there is an alternative mechanism for the transmission of these diseases that has not been considered in a modelling framework. This is transmission through ticks co-feeding on non-viraemic hosts. This paper extends a simple mathematical model to include this alternative transmission mechanism. The model is used to describe the dynamics of Louping ill virus in red grouse (the viraemic host) and hares (the non-viraemic host). However, these results are applicable to many other systems. The model is analysed using joint threshold density curves. It is found that the presence of a non-viraemic host allows the virus to persist more readily than it would in the presence of a host that simply amplified the tick population. More importantly, if the level of non-viraemic transmission is high enough the virus can persist in the absence of the viraemic host. This result has important implications for the control of tick borne diseases.
Brain activation to favorite music in healthy controls and depressed patients

Reward-processing neurocircuitry has been delineated using verbal or visual processing and/or decision-making tasks. We examined more basic processes of listening to enjoyable music in healthy and depressed patients. The paradigm was passive, individualized, and brief. Sixteen depressed and 15 control individuals provided favorite music and identified neutral music from selections provided. In the fMRI scanner, individuals heard their neutral and their favorite music for 3 min each. Favorite versus neutral music-listening contrasts showed greater activation in controls than depressed patients in medial orbital frontal cortex and nucleus accumbens/ventral striatum. Left medial prefrontal cortex activity was positively correlated with pleasure scores, whereas middle temporal cortex and globus pallidus were negatively correlated with pleasure. This paradigm activated neurocircuitry of reward processing and showed clinically meaningful alterations in depression.
Expression of the R 2 R 3-MYB Transcription Factor TaMYB 14 from Trifolium arvense Activates Proanthocyanidin Biosynthesis in the Legumes Trifolium repens and Medicago sativa 1 [ W ] [ OA ]

Proanthocyanidins (PAs) are oligomeric flavonoids and one group of end products of the phenylpropanoid pathway. PAs have been reported to be beneficial for human and animal health and are particularly important in pastoral agricultural systems for improved animal production and reduced greenhouse gas emissions. However, the main forage legumes grown in these systems, such as Trifolium repens and Medicago sativa, do not contain any substantial amounts of PAs in leaves. We have identified from the foliar PA-accumulating legume Trifolium arvense an R2R3-MYB transcription factor, TaMYB14, and provide evidence that this transcription factor is involved in the regulation of PA biosynthesis in legumes. TaMYB14 expression is necessary and sufficient to up-regulate late steps of the phenylpropanoid pathway and to induce PA biosynthesis. RNA interference silencing of TaMYB14 resulted in almost complete cessation of PA biosynthesis in T. arvense, whereas Nicotiana tabacum, M. sativa, and T. repens plants constitutively expressing TaMYB14 synthesized and accumulated PAs in leaves up to 1.8% dry matter. Targeted liquid chromatography-multistage tandem mass spectrometry analysis identified foliar PAs up to degree of polymerization 6 in leaf extracts. Hence, genetically modified M. sativa and T. repens plants expressing TaMYB14 provide a viable option for improving animal health and mitigating the negative environmental impacts of pastoral animal production systems.
Continuous subcutaneous insulin infusion: practical issues

The growing number of individuals with diabetes mellitus has prompted new way of treating these patients, continuous subcutaneous insulin infusion (CSII) or insulin pump therapy is an increasingly form of intensive insulin therapy. An increasing number of individuals with diabetes mellitus individuals of all ages have started using insulin pump therapy. Not everyone is a good candidate for insulin pump therapy, and the clinician needs to be able to determine which patients are able to master the techniques required and to watch for the adverse reactions that may develop. Insulin pump increases quality of life of patient with diabetes mellitus with increasing satisfaction with treatment and decrease impact of diabetes mellitus. Manual errors by insulin pump users may lead to hypo or hyperglycemia, resulting into diabetic ketoacidosis (DKA) sometimes. Some of practical aspect is associated with insulin pump therapy such as selection of candidates, handling of pump and selection of site, and pump setting, henceforth this review is prepared to explore and solve the practical problems or issues associated with pump therapy.
SAFA: semi-automated footprinting analysis software for high-throughput quantification of nucleic acid footprinting experiments.

Footprinting is a powerful and widely used tool for characterizing the structure, thermodynamics, and kinetics of nucleic acid folding and ligand binding reactions. However, quantitative analysis of the gel images produced by footprinting experiments is tedious and time-consuming, due to the absence of informatics tools specifically designed for footprinting analysis. We have developed SAFA, a semi-automated footprinting analysis software package that achieves accurate gel quantification while reducing the time to analyze a gel from several hours to 15 min or less. The increase in analysis speed is achieved through a graphical user interface that implements a novel methodology for lane and band assignment, called "gel rectification," and an optimized band deconvolution algorithm. The SAFA software yields results that are consistent with published methodologies and reduces the investigator-dependent variability compared to less automated methods. These software developments simplify the analysis procedure for a footprinting gel and can therefore facilitate the use of quantitative footprinting techniques in nucleic acid laboratories that otherwise might not have considered their use. Further, the increased throughput provided by SAFA may allow a more comprehensive understanding of molecular interactions. The software and documentation are freely available for download at http://safa.stanford. edu.
UPAYA MENGATASI KESULITAN SISWA DALAM OPERASI PERKALIAN DENGAN METODE LATIS

Salah satu permasalahan yang dihadapi siswa adalah lemahnya kemampuan siswa dalam operasi perkalian. Siswa kesulitan dalam operasi perkalian dengan menggunakan cara bersusun. Sejalan dengan itu, tujuan penelitian ini adalah untuk mengatasi kesulitan siswa dalam operasi perkalian dengan menerapkan metode perkalian latis. Jenis penelitian ini adalah penelitian deskriptif kualitatif yang dilakukan di kelas VII Sekolah Menengah Pertama dengan melibatkan enam siswa yang mengalami kesulitan dalam operasi perkalian. Penelitian ini dilaksanakan dalam 3 tahap yaitu: 1) perencanaan; 2) pelaksanaan yang terdiri dari 3 bagian: tes diagnostik, tes treatment, dan wawancara; 3) evaluasi. Hasil penelitian menunjukkan bahwa mereka sangat tertarik dan senang dengan metode ini. Mereka mampu menyelesaikan operasi perkalian dengan mudah, walaupun masih ada siswa yang kurang teliti. Namun, hal itu tidak membuat mereka merasa jenuh bahkan menjadi lebih semangat untuk memperbaiki kesalahannya. Siswa lebih memilih metode ini dalam menghitung perkalian dari pada metode yang dikenal sebelumnya. Kata kunci: kesulitan siswa, operasi perkalian, metode latis.
Comparing Effects of Dynamic Difficulty Adjustment Systems on Video Game Experience

Dynamic Difficulty Adjustment (DDA) is used by game designers to adaptively balance game challenge against player skill during play. While many DDA implementations exist, few comparative empirical studies, if any, have been done. This study investigates the effects of DDA systems on player experience through 3 conditions: no DDA, system-oriented ramping DDA (rDDA) and player-oriented DDA (pDDA). The presence of DDA was found to produce better overall game experiences. However, we found that players in the rDDA condition experienced less self-consciousness and more transformation of time but a lower sense of control compared to the players in the pDDA condition. Our findings provide new insight into DDA, demonstrating that while DDA systems can provide superior game experiences, specific drawbacks reduce their effectiveness. These considerations are of interest to interactive system designers, extending beyond games to areas where these types of adaptive systems have beneficial applications (e.g. physiotherapy or learning).
Learning Translation Models from Monolingual Continuous Representations

Translation models often fail to generate good translations for infrequent words or phrases. Previous work attacked this problem by inducing new translation rules from monolingual data with a semi-supervised algorithm. However, this approach does not scale very well since it is very computationally expensive to generate new translation rules for only a few thousand sentences. We propose a much faster and simpler method that directly hallucinates translation rules for infrequent phrases based on phrases with similar continuous representations for which a translation is known. To speed up the retrieval of similar phrases, we investigate approximated nearest neighbor search with redundant bit vectors which we find to be three times faster and significantly more accurate than locality sensitive hashing. Our approach of learning new translation rules improves a phrase-based baseline by up to 1.6 BLEU on Arabic-English translation, it is three-orders of magnitudes faster than existing semi-supervised methods and 0.5 BLEU more accurate.
Suboptimality Bounds for Stochastic Shortest Path Problems

We consider how to use the Bellman residual of the dynamic programming operator to compute suboptimality bounds for solutions to stochastic shortest path problems. Such bounds have been previously established only in the special case that "all policies are proper," in which case the dynamic programming operator is known to be a contraction, and have been shown to be easily computable only in the more limited special case of discounting. Under the condition that transition costs are positive, we show that suboptimality bounds can be easily computed even when not all policies are proper. In the general case when there are no restrictions on transition costs, the analysis is more complex. But we present preliminary results that show such bounds are possible.
Reactive Power Compensation in Single-Phase Operation of Microgrid

A coordinated control of distributed generators (DG) and distribution static compensator (DSTATCOM) in a microgrid is proposed in this paper. With high penetration of distributed sources and single-phase operation of the system, voltage unbalance can often go beyond the acceptable limit. With the feeders geographically spread out, it is not always possible to achieve reactive compensation at optimum location with the three-phase devices. In this paper, a simple control strategy for DSTATCOM with communication in loop is proposed. The proposed reactive compensation technique is based on the voltage sag and the power flow in the line. The power flow and the voltage at different locations of the feeders are communicated to the DSTATCOM to modulate the reactive compensation. The single-phase DSTATCOM compensates for the reactive power deficiency in the phase while the DGs supply “maximum available active power. ” During reactive power limit of the DG, the “maximum available active power” is fixed to a value lower than maximum active power to increase reactive power injection capability of the DGs. A primary control loop based on local measurement in the DSTATCOM always ensures a part of reactive compensation in case of communication failure. It is shown that the proposed method can always ensure to achieve acceptable voltage regulation. The data traffic analysis of the communication scheme and closed-loop simulation of power network and communication network are presented to validate the proposed method.
Punished: Policing the Lives of Black and Latino Boys

Preface Acknowledgments Part I Hypercriminalization 1 Dreams Deferred: The Patterns of Punishment in Oakland 2 The Flatlands of Oakland and the Youth Control Complex 3 The Labeling Hype: Coming of Age in the Era of Mass Incarceration 4 The Coupling of Criminal Justice and Community Institutions Part II Consequences 5 "Dummy Smart": Misrecognition, Acting Out, and "Going Dumb" 6 Proving Manhood: Masculinity as a Rehabilitative Tool 7 Guilty by Association: Acting White or Acting Lawful? Conclusion: Toward a Youth Support Complex Appendix: Beyond Jungle-Book Tropes Notes References Index About the Author