Miracle-dz/UniFAR-FTUs huggingface dataset:
Use of Yeast Mannoproteins by Oenococcus oeni during Malolactic Fermentation under Different Oenological Conditions

Oenococcus oeni is the main agent of malolactic fermentation in wine. This fermentation takes place after alcoholic fermentation, in a low nutrient medium where ethanol and other inhibitor compounds are present. In addition, some yeast-derived compounds such as mannoproteins can be stimulatory for O. oeni. The mannoprotein concentration in wine depends on the fermenting yeasts, and non-Saccharomyces in particular can increase it. As a result of the hydrolytic activity of O. oeni, these macromolecules can be degraded, and the released mannose can be taken up and used as an energy source by the bacterium. Here we look at mannoprotein consumption and the expression of four O. oeni genes related to mannose uptake (manA, manB, ptsI, and ptsH) in a wine-like medium supplemented with mannoproteins and in natural wines fermented with different yeasts. We observe a general gene upregulation in response to wine-like conditions and different consumption patterns in the studied media. O. oeni was able to consume mannoproteins in all the wines. This consumption was notably higher in natural wines, especially in T. delbrueckii and S. cerevisiae 3D wines, which presented the highest mannoprotein levels. Regardless of the general upregulation, it seems that mannoprotein degradation is more closely related to the fermenting medium.
Precise determination of the charm quark mass

The determination of the charm quark mass is now possible to 1% from QCD, with lattice QCD pushing the error down below 1%. I will describe the ingredients of this approach and how it can achieve this accuracy. Results for quark mass ratios, m_c/m_s and m_b/m_c, can also be determined to 1% from lattice QCD, allowing accuracy for the heavy quark masses to be leveraged into the light quark sector. I will discuss the prospects for, and importance of, improving results in future calculations.
A switch I mutant of Cdc42 exhibits decreased conformational freedom

Cdc42 is a Ras-related small G-protein, and functions as a molecular switch in signal transduction pathways linked with cell growth and differentiation. It is controlled by cycling between GTP-bound (active) and GDP-bound (inactive) forms. Nucleotide binding and hydrolysis are modulated by interactions with effectors and/or regulatory proteins. These interactions are centralized in two relatively flexible “Switch” regions as characterized by internal dynamics on multiple timescales (Loh et al., (2001) Biochemistry 40, 4590–4600), and this flexibility may be essential for protein interactions. In the Switch I region, Thr 35 seems critical for function, as it is completely invariant in Ras-related proteins. To investigate the importance of conformational flexibility in Switch I of Cdc42, we mutated threonine to alanine, determined the solution structure and characterized the backbone dynamics of the single-point mutant protein, Cdc42(T35A). Backbone dynamics data suggests that the mutation changes the timescale of the internal motions of several residues, with several resonances appearing not discernable in Cdc42 wild type (Adams and Oswald (2007) Biomolecular NMR Assignments 1, 225–227). The mutation does not appear to affect the thermal stability of Cdc42, and chymotrypsin digestion data further suggests that changes in conformational flexibility in Switch I slow proteolytic cleavage relative to wild type. In-vitro binding assays show reduced binding of Cdc42(T35A), relative to wild type, to a GTPase binding protein that inhibits GTP hydrolysis in Cdc42. These results suggest that the mutation of T 35 leads to the loss of conformational freedom in Switch I that could affect effector/regulatory protein interactions.
Symptom Clusters and Health-related Quality of Life in Patients with Chronic Stable Angina

Aim—This paper reports findings of a study to examine the independent contribution of chest pain, fatigue, and dyspnea to health-related quality of life in patients with chronic stable angina. Background—Patients with chronic stable angina experience poorer quality of life in multiple areas including physical and emotional health. Emerging evidence suggests the presence of concomitant symptoms, yet there are no systematic studies examining the impact of symptom clusters on quality of life in chronic angina patients. Method—Outpatients (n=134), recruited over a 16 month period in 2000 and 2001, with confirmed coronary heart disease and chronic angina completed reliable and valid questionnaires measuring chest pain frequency, fatigue, dyspnea and quality of life. Hierarchical multiple linear regression was used to examine the symptom cluster of chest pain frequency, fatigue, and dyspnea in predicting quality of life. Results—The sample was predominantly white (74.6%), males (59.7%) with a mean age of 63.4 (SD 12.12) years. Controlling for age, gender, social status, and comorbidities, the symptom cluster of chest pain frequency, dyspnea, and fatigue accounted for significant increase in unadjusted R2, (F of Δ, p < .05) for the models predicting physical limitation (R2 Δ 24.1%), disease perception (R2 Δ 24.6%), Short Form-36 Physical Component Score (R2 Δ 24.3%) and Mental Component Score (R2 Δ 07.0%). Conclusion—Symptom assessment and management of patients with chronic stable angina should involve multiple symptoms. Greater fatigue predicted poorer quality of life in multiple areas. As a possible indicator of depression, it warrants further assessment and follow-up. Corresponding Author Contact Information: Laura P. Kimble, PhD, RN, Professor and Piedmont Healthcare Endowed Chair in Nursing, Georgia Baptist College of Nursing of Mercer University, 3001 Mercer University Drive, Atlanta, GA 30341 U.S. A. Telephone: 678-547-6781, Kimble_LP@mercer.edu. Conflict of interest: No conflict of interest has been declared by the authors. Author Contributions: LPK, SBD, WSW, DBM, SFM & OLS were responsible for the study conception and design SFM performed the data collection LPK performed the data analysis. LPK was responsible for the drafting of the manuscript. SBD, WSW, DBM, SFM & OLS made critical revisions to the paper for important intellectual content. LPK provided statistical expertise. LPK, SBD, WSW, DBM & OLS obtained funding LPK, SBD, DBM & OLS provided administrative, technical or material support. LPK supervised the study NIH Public Access Author Manuscript J Adv Nurs. Author manuscript; available in PMC 2012 May 1. Published in final edited form as: J Adv Nurs. 2011 May ; 67(5): 1000–1011. doi:10.1111/j.1365-2648.2010. 05564.x. N IH PA Athor M anscript N IH PA Athor M anscript N IH PA Athor M anscript
Constraint-handling techniques used with evolutionary algorithms

Evolutionary Algorithms (EAs), when used for global optimization, can be seen as unconstrained optimization techniques. Therefore, they require an additional mechanism to incorporate constraints of any kind (i.e., inequality, equality, linear, nonlinear) into their fitness function. Although the use of penalty functions (very popular with mathematical programming techniques) may seem an obvious choice, this sort of approach requires a careful fine tuning of the penalty factors to be used. Otherwise, an EA may be unable to reach the feasible region (if the penalty is too low) or may reach quickly the feasible region but being unable to locate solutions that lie in the boundary with the infeasible region (if the penalty is too severe). This has motivated the development of a number of approaches to incorporate constraints into the fitness function of an EA. This tutorial will cover the main proposals in current use, including novel approaches such as the use of tournament rules based on feasibility, multiobjective optimization concepts, hybrids with mathematical programming techniques (e.g., Lagrange multipliers), cultural algorithms, and artificial immune systems, among others. Other topics such as the importance of maintaining diversity, current benchmarks and the use of alternative search engines (e.g., particle swarm optimization, differential evolution, evolution strategies, etc.) will be also discussed (as time allows).
A New Approach to Producing Functional G α Subunits Yields the Activated and Deactivated Structures of G α 12/13 Proteins

Summary The oncogenic G 12/13 subfamily of heterotrimeric G proteins transduces extracellular signals that regulate the actin cytoskeleton, cell cycle progression, and gene transcription. Previously, structural analyses of fully-functional G α 12/13 subunits have been hindered by insufficient amounts of homogeneous, functional protein. Herein we report that substitution of the N-terminal helix of G α i1 for the corresponding region of G α 12 or G α 13 generated soluble chimeric subunits (G α i/12 and G α i/13 ) that could be purified in sufficient amounts for crystallographic studies. Each chimera bound guanine nucleotides, G βγ subunits and effector proteins, and exhibited GAP responses to p115RhoGEF and leukemia-associated RhoGEF. Like their wild-type counterparts, G α i/13 , but not G α i/12 , stimulated the activity of p115RhoGEF. Crystal structures of the G α i/12 ·GDP·AlF 4 − and G α i/13 ·GDP complexes were determined using diffraction data extending to 2.9 and 2.0 Å, respectively. These structures reveal not only the native structural features of G α 12 and G α 13 subunits, which are expected to be important for their interactions with GPCRs and effectors such as G α regulated RhoGEFs, but also novel conformational changes that are likely coupled to GTP hydrolysis in the G α 12/13 class of heterotrimeric G proteins. Heterotrimeric proteins (RH domains) have distinct functions.
EXPRESSION PROFILING OF TGFß SUPERFAMILY GENES IN DEVELOPING OROFACIAL TISSUE

Background—Numerous signaling molecules have been shown to participate in the dynamic process of orofacial development. Amongst these signal mediators, members of the transforming growth factor ß (TGFß) superfamily have been shown to play critical roles. Developing orofacial tissue expresses TGFß and BMP mRNAs, their protein isoforms and TGFßand BMP-specific receptors. All these molecules display unique temporo-spatial patterns of expression in embryonic orofacial tissue, suggesting functional roles in orofacial development. For example, the TGFßs and BMPs regulate maxillary mesenchymal cell proliferation and extracellular matrix synthesis. This is particularly noteworthy in that perturbation of either process results in orofacial clefting. Although the cellular and phenotypic effects of the TGFß superfamily of growth factors on embryonic orofacial tissue have been extensively studied, the specific genes that function as effectors of these cytokines in orofacial development has not been well defined.
Agent-based inter-organizational systems in advanced logistics operations

textabstract“Agent-based Inter-organizational Systems (ABIOS) in Advanced Logistics Operations” explores the concepts, the design, and the role and impact of agent-based systems to improve coordination and performance of logistics operations. The dissertation consists of one conceptual study and three empirical studies. The empirical studies apply various research methods such as a multiple-case study research, coordination mechanism design, and predictive analytics using big data. The conceptual study presents a theoretical exploration and synthesis explaining the demand for inter-organizational systems (IOS) and the corresponding IOS functionalities. The first empirical study presents a multiple-case study exploring real-life ABIOS implementations in the warehousing and transportation business. The second empirical study provides an auction based coordination mechanism design for the container’s pick-up/delivery appointment reservation problem that involves the seaports and drayage operators. The third empirical study presents a seaport service rate prediction system that could help drayage operators to improve their predictions of the duration of the pick-up/delivery operations at a seaport by using the subordinate trucks’ trajectory data. Based on these studies, the dissertation offers new insights on the role of inter-organizational systems in mitigating coordination equivocality and uncertainties; the interplay among the ABIOS applications, required structural adjustments, and the potential of business performance improvement opportunities; and the development of two ABIOS prototypes: an auction based coordination mechanism and a predictive analytics application based on big data.
Contrasting Effects of the SATBI Core Nuclear Matrix Attachment Region and Flanking Sequences of the Keratin 18 Gene in Transgenic Mice

The 2.3 kb and 3.5 kb of DNA that flank the human keratin 18 (K18) gene and synthetic nuclear matrix attachment regions (MAR) composed of the binding sites for the SATB1 nuclear protein were fused to a reporter gene that utilizes the mouse metallothionein promoter and the human growth hormone gene (MThGH). Transgenic mice were generated from both constructions and the control MThGH gene to test K18 and SATB1 MAR sequences for the ability to insulate the reporter gene from integration site-specific position effects. The MThGH control gene was variably expressed in brain, heart, intestine, kidney, liver, and testes, confirming previous studies. In contrast, the MThGH gene insulated by the K18 flanking sequences was expressed in the same tissues of four independent transgenic animals at levels correlated with the copy number except for intestine. The average level of expression on a per gene basis of the K18 insulated gene was from 9- to 49-fold higher than the control. The MThGH gene linked to the SATB1 MAR sequences was completely repressed in the brains and kidneys of all six transgenic mice. However, expression was nearly as efficient in testes as the K18-insulated gene. Both the SATB1 MAR and the K18 flanking sequences confer position-independent transcriptional status on the reporter gene in some or many tissues. However, the effects are stimulatory for the K18 elements and generally suppressive for the SATB1 MAR elements.
FROM X TO Y: THE 'COMPLETE PATH' CONSTRUCTION IN BASQUE

In Basque, there is recurrent tendency to express both the source and goal of movement for the description of translational motion even in cases where one of these elements is pleonastic. This construction called ‘Complete Path’ (Ibarretxe-Antunano 2002) shows up not only in physical description of motion but also in a good number of different metaphorical and idiomatic expressions. At first sight, these metaphorical expressions do not seem to follow any clear pattern: some expressions express ‘quickness’, some others ‘period of time’, and some others ‘manner’. In this paper, we argue against this position. We propose that all these expressions form a coherent, structured, and motivated group. We will base this claim on the following theoretical assumptions: (i) the ‘Complete path’ is a ‘construction’ in terms of Goldberg’s (1995) and Fillmore and Kay’s (1995) construction grammar; (ii) these meanings are the result of what Fauconnier and Turner (1998, 2002) called conceptual integration. The physical experience of a translational motion from one place to another is blended with whatever the semantic content of the landmark denotes.
Advanced Probabilistic Simulation of NPP Fires

The consequences of fires at NPPs can be estimated using the numerical simulation. When combined with Monte Carlo technique, the probability of target events can be calculated. The computational cost related to the use of most advanced fire models has prevented their application in this probabilistic manner. In this work, a new technique, based on an intuitive approach, is proposed. The technique allows the use of two different models in the same Monte Carlo simulation, and is therefore called Two-Model Monte Carlo (TMMC). In TMMC, simulations are first performed using both models in relatively small number of points of the random space, and the scaling functions are formed. Full Monte Carlo is then performed using the faster but less accurate model, and the results are corrected using the scaling functions. The performance of the numerical technique is studied in a simple room fire scenario, where two-zone and computational fluid dynamics (CFD) models are used. TMMC can reduce the computational cost with a factor of 30, compared to a full Monte Carlo using CFD. As a real NPP fire scenario, the distribution of component failure time is calculated in a relay room fire. In this application, CFD is used in both models but the difference in accuracy and computational cost is achieved by the refinement of the computational mesh.
Studies on the specificity of acetylaminoacyl- peptide hydrolase

In a continuing attempt to explore the types of specificity determinants that may affect protein-protein (peptide) interactions, a number of short (2-5 residues) acetylated peptides have been compared as substrates for the enzyme acetylaminoacyl-peptide hydrolase (EC 3.4.19.1). The reference substrate was Ac-AAAA, and most of the other substrates were derived from this basic structure by single amino acid substitutions. The K , and k,, for the different substrates were determined by standard steady-state kinetics, and the corresponding AAGTx value derived from k,,/K,,, was used for the comparison, setting AAGTt for Ac-AAAA equal to 0. The best substrates were found to be those containing negative charges (Asp > Glu) or aromatic residues in positions l', 2: or 3' (AAG,t values of 2-5 kJ); the negative charge provided by the C-terminus of the substrate also appears to be important, since the amide and 0-Me ester derivatives caused a change in AAGTx values of -7 to -8 kJ from the reference peptide. The stimulating effect of the negative charges is consistent with the inhibitory effect of positive charges in similar peptides (Krishna RG, Wold F, 1992, Protein Sci 1:582-589), and the proposed active site model incorporates subsites for both charge-charge and hydrophobic interactions. In assessing all the data, it is clear that the properties of the individual substrates reflect the total make-up of each peptide and not only the effect of a single residue in a given position. Thus, while the peptides with single Asp or Phe substitutions in l', 2: and 3' gave AAGTr values of 3-5 kJ, the peptide containing all 3 modifications, Ac-ADDF, gave only 1 kJ. Similarly, Ac-TAAA was a poor substrate and Ac-GAAA was not cleaved at all in this study, while in the past other peptides such as Ac-TGG and Ac-GGG have been found to be excellent and reasonably good substrates, respectively. Although the rate differences observed in this work are minor, they nevertheless appear to reflect the kind of structural detail that is involved in determining the specificity of protein-protein (peptide) interactions.
Metabolic Syndrome and Salt-Sensitivity of Blood Pressure among Persons without Diabetes

Jing Chen, MD, MSc1,2, Dongfeng Gu, MD, PhD3, Jianfeng Huang, MD3, DC Rao, PhD4, Cashell E. Jaquish, PhD5, James E. Hixson, PhD6, Chung-Shiuan Chen, MS2, Jichun Chen, MD3, Fanghong Lu, MD7, Dongsheng Hu, MD8, Treva Rice, PhD4, Tanika N. Kelly, MPH2, L. Lee Hamm, MD1, Paul K. Whelton, MD, MSc9, and Jiang He, MD, PhD1,2 for the GenSalt Collaborative Research Group* 1 Department of Medicine and Tulane Hypertension and Renal Center of Excellence, Tulane University School of Medicine, New Orleans, LA, USA
Mixed-Timescale Deep-Unfolding for Joint Channel Estimation and Hybrid Beamforming

In massive multiple-input multiple-output (MIMO) systems, hybrid analog-digital beamforming is an essential technique for exploiting the potential array gain without using a dedicated radio frequency chain for each antenna. However, due to the large number of antennas, the conventional channel estimation and hybrid beamforming algorithms generally require high computational complexity and signaling overhead. In this work, we propose an end-to-end deep-unfolding neural network (NN) joint channel estimation and hybrid beamforming (JCEHB) algorithm to maximize the system sum rate in time-division duplex (TDD) massive MIMO. Specifically, the recursive least-squares (RLS) algorithm and stochastic successive convex approximation (SSCA) algorithm are unfolded for channel estimation and hybrid beamforming, respectively. In order to reduce the signaling overhead, we consider a mixed-timescale hybrid beamforming scheme, where the analog beamforming matrices are optimized based on the channel state information (CSI) statistics offline, while the digital beamforming matrices are designed at each time slot based on the estimated low-dimensional equivalent CSI matrices. We jointly train the analog beamformers together with the trainable parameters of the RLS and SSCA induced deep-unfolding NNs based on the CSI statistics offline. During data transmission, we estimate the low-dimensional equivalent CSI by the RLS induced deep-unfolding NN and update the digital beamformers. In addition, we propose a mixed-timescale deep-unfolding NN where the analog beamformers are optimized online, and extend the framework to frequency-division duplex (FDD) systems where channel feedback is considered. Simulation results show that the proposed algorithm can significantly outperform conventional algorithms with reduced computational complexity and signaling overhead.
TURJUMAN: A Public Toolkit for Neural Arabic Machine Translation

We present TURJUMAN, a neural toolkit for translating from 20 languages into Modern Standard Arabic (MSA). TURJUMAN exploits the recently-introduced text-to-text Transformer AraT5 model, endowing it with a powerful ability to decode into Arabic. The toolkit offers the possibility of employing a number of diverse decoding methods, making it suited for acquiring paraphrases for the MSA translations as an added value. To train TURJUMAN, we sample from publicly available parallel data employing a simple semantic similarity method to ensure data quality. This allows us to prepare and release AraOPUS-20, a new machine translation benchmark. We publicly release our translation toolkit (TURJUMAN) as well as our benchmark dataset (AraOPUS-20).
Resolving the Human Subjects Status of Machine Learning's Crowdworkers

In recent years, machine learning (ML) has relied heavily on crowdworkers both for building datasets and for addressing research questions requiring human interaction or judgment. The diversity of both the tasks performed and the uses of the resulting data render it difficult to determine when crowdworkers are best thought of as workers versus human subjects. These difficulties are compounded by conflicting policies, with some institutions and researchers regarding all ML crowdworkers as human subjects and others holding that they rarely constitute human subjects. Notably few ML papers involving crowdwork mention IRB oversight, raising the prospect of non-compliance with ethical and regulatory requirements. We investigate the appropriate designation of ML crowdsourcing studies, focusing our inquiry on natural language processing to expose unique challenges for research oversight. Crucially, under the U.S. Common Rule, these judgments hinge on determinations of aboutness , concerning both whom (or what) the collected data is about and whom (or what) the analysis is about. We highlight two challenges posed by ML: the same set of workers can serve multiple roles and provide many sorts of information; and ML research tends to embrace a dynamic workflow, where research questions are seldom stated ex ante and data sharing opens the door for future studies to aim questions at different targets. Our analysis exposes a potential loophole in the Common Rule, where researchers can elude research ethics oversight by splitting data collection and analysis into distinct studies. Finally, we offer several policy recommendations to address these concerns.