Miracle-dz/UniFAR-FTUs huggingface dataset:
Shifting the Fermentative/Oxidative Balance in Saccharomyces cerevisiae by Transcriptional Deregulation of Snf1 via Overexpression of the Upstream Activating Kinase Sak1p

ABSTRACT With the aim to reduce fermentation by-products and to promote respiratory metabolism by shifting the fermentative/oxidative balance, we evaluated the constitutive overexpression of the SAK1 and HAP4 genes in Saccharomyces cerevisiae. Sak1p is one of three kinases responsible for the phosphorylation, and thereby the activation, of the Snf1p complex, while Hap4p is the activator subunit of the Hap2/3/4/5 transcriptional complex. We compared the physiology of a SAK1-overexpressing strain with that of a strain overexpressing the HAP4 gene in wild-type and sdh2 deletion (respiratory-deficient) backgrounds. Both SAK1 and HAP4 overexpressions led to the upregulation of glucose-repressed genes and to reduced by-product formation rates (ethanol and glycerol). SAK1 overexpression had a greater impact on growth rates than did HAP4 overexpression. Elevated transcript levels of SAK1, but not HAP4, resulted in increased biomass yields in batch cultures grown on glucose (aerobic and excess glucose) as well as on nonfermentable carbon sources. SAK1 overexpression, but not the combined overexpression of SAK1 and HAP4 or the overexpression of HAP4 alone, restored growth on ethanol in an sdh2 deletion strain. In glucose-grown shake flask cultures, the sdh2 deletion strain with SAK1 and HAP4 overexpression produced succinic acid at a titer of 8.5 g liter−1 and a yield of 0.26 mol (mol glucose)− 1 within 216 h. We here report for the first time that a constitutively high level of expression of SAK1 alleviates glucose repression and shifts the fermentative/oxidative balance under both glucose-repressed and -derepressed conditions.
Learning Classifiers When the Training Data Is Not IID

Most methods for classifier design assume that the training samples are drawn independently and identically from an unknown data generating distribution, although this assumption is violated in several real life problems. Relaxing this i.i. d. assumption, we consider algorithms from the statistics literature for the more realistic situation where batches or sub-groups of training samples may have internal correlations, although the samples from different batches may be considered to be uncorrelated. Next, we propose simpler (more efficient) variants that scale well to large datasets; theoretical results from the literature are provided to support their validity. Experimental results from real-life computer aided diagnosis (CAD) problems indicate that relaxing the i.i. d. assumption leads to statistically significant improvements in the accuracy of the learned classifier. Surprisingly, the simpler algorithm proposed here is experimentally found to be even more accurate than the original version.
Telos: enabling ultra-low power wireless research

We present Telos, an ultra low power wireless sensor module ("mote") for research and experimentation. Telos is the latest in a line of motes developed by UC Berkeley to enable wireless sensor network (WSN) research. It is a new mote design built from scratch based on experiences with previous mote generations. Telos' new design consists of three major goals to enable experimentation: minimal power consumption, easy to use, and increased software and hardware robustness. We discuss how hardware components are selected and integrated in order to achieve these goals. Using a Texas Instruments MSP430 microcontroller, Chipcon IEEE 802.15. 4-compliant radio, and USB, Telos' power profile is almost one-tenth the consumption of previous mote platforms while providing greater performance and throughput. It eliminates programming and support boards, while enabling experimentation with WSNs in both lab, testbed, and deployment settings.
Two for the price of one: composing partial evaluation and compilation

One of the flagship applications of partial evaluation is compilation and compiler generation. However, partial evaluation is usually expressed as a source-to-source transformation for high-level languages, whereas realistic compilers produce object code.We close this gap by composing a partial evaluator with a compiler by automatic means. Our work is a successful application of several meta-computation techniques to build the system, both in theory and in practice. The composition is an application of deforestation or fusion.The result is a run-time code generation system built from existing components. Its applications are numerous. For example, it allows the language designer to perform interpreter-based experiments with a source-to-source version of the partial evaluator before building a realistic compiler which generates object code automatically.
Two Conserved Cysteine Residues Are Required for the Masculinizing Activity of the Silkworm Masc Protein*

Background: The functional domains of the silkworm masculinizing protein Masc are unknown. Results: The essential region and residues involved in the masculinizing activity of the Masc protein are identified. Conclusion: Masc functions as the masculinizing protein via its C-terminal region but not two zinc finger domains in the N-terminal region. Significance: Our study suggests the mode of action of the masculinizing protein. We have recently discovered that the Masculinizer (Masc) gene encodes a CCCH tandem zinc finger protein, which controls both masculinization and dosage compensation in the silkworm Bombyx mori. In this study, we attempted to identify functional regions or residues that are required for the masculinizing activity of the Masc protein. We constructed a series of plasmids that expressed the Masc derivatives and transfected them into a B. mori ovary-derived cell line, BmN-4. To assess the masculinizing activity of the Masc derivatives, we investigated the splicing patterns of B. mori doublesex (Bmdsx) and the expression levels of B. mori IGF-II mRNA-binding protein, a splicing regulator of Bmdsx, in Masc cDNA-transfected BmN-4 cells. We found that two zinc finger domains are not required for the masculinizing activity. We also identified that the C-terminal 288 amino acid residues are sufficient for the masculinizing activity of the Masc protein. Further detailed analyses revealed that two cysteine residues, Cys-301 and Cys-304, in the highly conserved region among lepidopteran Masc proteins are essential for the masculinizing activity in BmN-4 cells. Finally, we showed that Masc is a nuclear protein, but its nuclear localization is not tightly associated with the masculinizing activity.
Methyl 4-hydroxy-1,1-dioxo-2-(2-phenylethyl)-2H-1λ6,2-benzothiazine-3-carboxylate

In the title compound, C18H17NO5S, the thiazine ring adopts a half-chair conformation and the dihedral angle between the aromatic rings is 79.41 (6)°. An intramolecular O—H⋯O hydrogen bond generates an S(6) ring. In the crystal, molecules are linked by weak C—H⋯O interactions resulting in infinite sheets along the b and c axes.
Liver transplantation for neonatal hemochromatosis: Analysis of the UNOS database

NH is the most common identifiable cause of ALF in the neonate. LT is the definitive treatment for neonates with NH who have failed medical therapy. Our aim was to determine the outcomes of LT in infants with NH. Patients (less than one yr of age) with NH who were listed for LT and patients who underwent LT between 1994 and 2013 were identified from the UNOS database for analysis. Risk factors for death and graft loss were analyzed by multivariate logistic regression. Thirty‐eight infants with NH with a total of 43 transplants were identified. One‐ and five‐yr patient and graft survival were 84.2%, 81.6%, 71.1%, and 68.4%, respectively. The outcomes for NH were not significantly different when compared to the same age‐matched recipients with other causes of ALF. There were no statistically significant risk factors identified for graft loss or death. Ninety infants with NH were listed for LT. Reasons for removal included transplanted (49%), death (27%), too sick to transplant (7%), and improved status (13%). LT for infants with NH has a high rate of graft loss and death; however, outcomes are comparable to the same age‐matched recipients with other causes of ALF.
Numerical analysis of unit cell models for orthopedic applications

For orthopedic applications 3D metal printing delivers flexible and tailor-made solutions. The greatest advantage of the additive manufacturing is that patient-specific implants can be manufactured. Determination of compressive properties of implant structure by numerical way is a demanding engineering task and it is indispensable for design purposes. In design of load-bearing biomedical implants the elastic behavior under working circumstances has to be considered. The professional literature offers different unit cell models to represent trabecular structures. In this paper the cubic open cell structures are established using CAD application and linear-elastic finite element simulations are performed. The aim of the research is to compare the material response of the investigated geometrical models.
Local and regional controls of phylogenetic structure at the high-latitude range limits of corals

Understanding how range-edge populations will respond to climate change is an urgent research priority. Here, we used a phylogenetic community ecology approach to examine how ecological and evolutionary processes shape biodiversity patterns of scleractinian corals at their high-latitude range limits in eastern Australia. We estimated phylogenetic signal in seven ecologically important functional traits and conducted tests of phylogenetic structure at local and regional scales using the net relatedness (NRI) and nearest taxon indices (NTI) for the presence/absence and abundance data. Regional tests showed light phylogenetic clustering, indicating that coral species found in this subtropical-to-temperate transition zone are more closely related to each other than are species on the nearby, more northerly Great Barrier Reef. Local tests revealed variable patterns of phylogenetic clustering and overdispersion and higher than expected phylogenetic turnover among sites. In combination, these results are broadly consistent with the hierarchical filtering model, whereby species pass through a regional climatic filter based on their tolerances for marginal conditions and subsequently segregate into local assemblages according to the relative strength of habitat filtering and species interactions. Conservatism of tested traits suggests that corals will likely track their niches with climate change. Nevertheless, high turnover of lineages among sites indicates that range shifts will probably vary among species and highlights the vulnerability and conservation significance of high-latitude reefs.
UM‐SCC‐104: A New human papillomavirus‐16–positive cancer stem cell–containing head and neck squamous cell carcinoma cell line

Few human papillomavirus (HPV)(+) head and neck squamous cell carcinoma (HNSCC) cell lines exist. We established University of Michigan‐squamous cell carcinoma‐104 (UM‐SCC‐104), a new HPV(+) HNSCC cell line from a recurrent oral cavity tumor, and characterized it for the presence of cancer stem cells (CSCs).
Vision in natural and virtual environments

Our knowledge of the way that the visual system operates in everyday behavior has, until recently, been very limited. This information is critical not only for understanding visual function, but also for understanding the consequences of various kinds of visual impairment, and for the development of interfaces between human and artificial systems. The development of eye trackers that can be mounted on the head now allows monitoring of gaze without restricting the observer's movements. Observations of natural behavior have demonstrated the highly task-specific and directed nature of fixation patterns, and reveal considerable regularity between observers. Eye, head, and hand coordination also reveals much greater flexibility and task-specificity than previously supposed. Experimental examination of the issues raised by observations of natural behavior requires the development of complex virtual environments that can be manipulated by the experimenter at critical points during task performance. Experiments where we monitored gaze in a simulated driving environment demonstrate that visibility of task relevant information depends critically on active search initiated by the observer according to an internally generated schedule, and this schedule depends on learnt regularities in the environment. In another virtual environment where observers copied toy models we showed that regularities in the spatial structure are used by observers to control eye movement targeting. Other experiments in a virtual environment with haptic feedback show that even simple visual properties like size are not continuously available or processed automatically by the visual system, but are dynamically acquired and discarded according to the momentary task demands.
Planetary Detection Efficiency of the Magnification 3000 Microlensing Event OGLE-2004-BLG-343

OGLE-2004-BLG-343 was a microlensing event with peak magnification Amax = 3000 ± 1100, by far the highest magnification event ever analyzed and hence potentially extremely sensitive to planets orbiting the lens star. Due to human error, intensive monitoring did not begin until 43 minutes after peak, at which point the magnification had fallen to A ~ 1200, still by far the highest ever observed. As the light curve does not show significant deviations due to a planet, we place upper limits on the presence of such planets by extending the method of Yoo et al. (2004b), which combines light-curve analysis with priors from a Galactic model of the source and lens populations, to take account of finite-source effects. This is the first event so analyzed for which finite-source effects are important, and hence we develop two new techniques for evaluating these effects. Somewhat surprisingly, we find that OGLE-2004-BLG-343 is no more sensitive to planets than two previously analyzed events with Amax ~ 100, despite the fact that it was observed at ~12 times higher magnification. However, we show that had the event been observed over its peak, it would have been sensitive to almost all Neptune-mass planets over a factor of 5 of projected separation and even would have had some sensitivity to Earth-mass planets. This shows that some microlensing events being detected in current experiments are sensitive to very low mass planets. We also give suggestions on how extremely high magnification events can be more promptly monitored in the future.
Electronic and optical properties of black phosphorus doped with Au, Sn and I atoms

Abstract In this study, the electronic and the optical properties of monolayer black phosphorus (BP) doped with Gold (Au), Tin (Sn) and Iodine (I) atoms have been investigated by the density-functional theory (DFT) method. In the calculations, the electronic and the optical properties of monolayer BP have been substantially changed with doping. Monolayer BP has a narrow bandgap as 0.85 eV, BP doped with these atoms, results in a metallic behaviour and nearly spin gapless band gap behaviour. The dielectric constant of BP which shows anisotropic optical properties due to different edge states as zigzag and armchair has been changed with doping especially with Au.
Platelet rich fibrin and alloplast in the treatment of intrabony defect

Periodontal regeneration is defined as the reproduction or reconstitution of a lost or injured part to restore the architecture and function of the periodontium. The ultimate goal of periodontal therapy is to regenerate the lost periodontal tissues caused by periodontitis. The most positive outcome of periodontal regenerative procedures in intra bony defect has been achieved with bone grafts. For complete regeneration, delivery of growth factors in a local environment holds a great deal in adjunct to bone grafts. Platelet rich fibrin (PRF) is considered as second generation platelet concentrate, consisting of viable platelets, releasing various growth factors. Hence, this case report aims to investigate the clinical and radiological (bone fill) effectiveness of autologous PRF along with the use of alloplastic bone mineral in the treatment of intra bony defects.
Dose response of whole-grain biomarkers: alkylresorcinols in human plasma and their metabolites in urine in relation to intake.

BACKGROUND Alkylresorcinols (ARs), phenolic lipids almost exclusively present in the outer parts of wheat and rye grains in commonly consumed foods, have been proposed as specific dietary biomarkers of whole-grain wheat and rye intakes. OBJECTIVE The objective was to assess the dose response of plasma ARs and the excretion of 2 recently discovered AR metabolites in 24-h urine samples in relation to AR intake and to establish a pharmacokinetic model for predicting plasma AR concentration. DESIGN Sixteen subjects were given rye bran flakes containing 11, 22, or 44 mg total ARs 3 times daily during week-long intervention periods separated by 1-wk washout periods in a nonblinded randomized crossover design. Blood samples were collected at baseline, after the 1-wk run-in period, and after each treatment and washout period. Two 24-h urine samples were collected at baseline and after each treatment period. RESULTS Plasma AR concentrations and daily excretion of 2 urinary AR metabolites increased with increasing AR dose (P < 0.001). Recovery of urinary metabolites in 24-h samples decreased with increasing doses from approximately 90% to approximately 45% in the range tested. A one-compartment model with 2 absorption compartments with different lag times and absorption rate constants adequately predicted plasma AR concentrations at the end of each intervention period. CONCLUSION Both plasma AR concentrations and urinary metabolites in 24-h samples showed a dose-response relation to increased AR intake, which strongly supports the hypothesis that ARs and their metabolites may be useful as biomarkers of whole-grain wheat and rye intakes.
Improved conditions for silver–ammonia staining of DNA in polyacrylamide gel

An improved silver–ammonia staining method for DNA on polyacrylamide gels is described. In this method, staining of DNA using silver–ammonia complex allows high sensitivity, low cost, low toxicity, and simple protocol without requiring fixation and sensitization steps. The protocol takes less than 40 min to complete, with a detection limit of 1.5 pg of single DNA band on polyacrylamide gels, approximately 30‐fold higher than that of original silver–ammonia staining method. Furthermore, this novel technique not only exhibits high sensitivity for large DNA fragment, but also shows a better trend to detect low‐base‐pair DNA compared with other silver staining methods.
An efficient development of 3D surface registration by Point Cloud Library (PCL)

This paper presents how to utilize the open source Point Cloud library (PCL) to develop a series of computational registration processes efficiently and robustly. The registration is the key process of the Digital Face-Inspection (DFI) system. In 2009, the DFI system was developed to assist dentists to detect deviations of patients' face shapes before/after an orthodontic treatment. The system combined the technologies of 3D scanning and Reverse Engineering together to achieve the goal of creating a better quality environment. Regarding the visual analysis made by the DFI system, dentists can adjust their treatments to guarantee that their treatments are on the right track. This is definitely very helpful to create a high-quality dental environment. The inputs of the DFI system are a set of point clouds generated by 3D scanning systems. The data type of point cloud present an object by a huge amount of surface points. A completed DFI process requires two scanning independent scanning routines and those scanning routines generated point cloud by their reference coordinate systems. This event causes that generated point clouds can't be applied into the deviation analysis directly. Before the analysis, the DFI system introduced the Iterative Closest Point (ICP) algorithm to align two point clouds as close as possible. This is to force two point clouds in a same coordinate system. However, the ICP algorithm is a local operation process. Therefore, a coarse registration is required for finding an optimal initial alignment. The registration includes a lot of computational algorithms and makes the DFI development very complicated. Fortunately, an open source called Point Cloud Library is available for helping us to develop this registration easily and efficiently. PCL collected hundreds of functions and algorithms for handling point cloud data in various applications. This paper demonstrates how to introduce PCL to build up the DFI system. In addition, we also presented how to utilize PCL to improve the efficiency of the DFI system.
Homology Modelling of the GABA Transporter and Analysis of Tiagabine Binding

A homology model of the human GABA transporter (GAT‐1) based on the recently reported crystal structures of the bacterial leucine transporter from Aquifex aeolicus (LeuT) was developed. The stability of the resulting model embedded in a membrane environment was analyzed by extensive molecular dynamics (MD) simulations. Based on docking studies and subsequent MD simulations of three compounds, the endogenous ligand GABA and two potent inhibitors, (R)‐nipecotic acid and the anti‐epilepsy drug tiagabine, various binding modes were identified and are discussed. Whereas GABA and (R)‐nipecotic acid, which are both substrates, are stabilised with residues located deep inside the occluded state binding pocket (including residues Tyr 60 and Ser 396), tiagabine, which contains a large aliphatic side chain, is stabilised in a binding mode that extends from the substrate binding pocket (i.e., stabilised by Phe 294) to the extracellular vestibule, where the side chain is stabilised by aliphatic residues. The tiagabine binding mode, reaching from the substrate binding site to the extracellular vestibule, forces the side chain of Phe 294 to adopt a distinct conformation from that found in the occluded conformation of the transporter. Hence, in presence of tiagabine, GAT‐1 is constrained in an open‐to‐out conformation. Our results may be of particular interest for the design of new GAT‐1 inhibitors.
Federated End-to-End Authentication for the Constrained Internet of Things Using IBC and ECC

Authentication of smart objects is a major challenge for the Internet of Things (IoT), and has been left open in DTLS. Leveraging locally managed IPv6 addresses with identity-based cryptography (IBC), we propose an efficient end-to-end authentication that (a) assigns a robust and deployment-friendly federation scheme to gateways of IoT subnetworks, and (b) has been evaluated with a modern twisted Edwards elliptic curve cryptography (ECC). Our early results demonstrate feasibility and promise efficiency after ongoing optimizations.