Miracle-dz/UniFAR-FTUs huggingface dataset:
High performance phylogenetic inference

Phylogenetic analysis is an integral part of many biological research programs. In essence, it is the study of gene genealogy. It is the study of gene mutation and the generational relationships. Phylogenetic analysis is being used in many diverse areas such as human epidemiology, viral transmission, biogeography, and systematics. Researchers are now commonly generating many DNA sequences from many individuals, thus creating very large data sets. However, our ability to analyze the data has not kept pace with data generation, and phylogenetics has now reached a crossroads where we cannot effectively analyze the data we generate. The chief challenge of phylogenetic systematics in the next century will be to develop algorithms and search strategies to effectively analyze large data sets. The crux of the computational problem is that the actual landscape of possible topologies can be extraordinarily difficult to evaluate with large data sets. The parsimony ratchet is actually a family of iterative tree search methods that use a statistical approach to sampling tree islands and ultimately finding the most parsimonious trees for a data set. Each iteration of the parsimony ratchet may occur in parallel as there is no direct dependency between iterations. The authors' implementation of the parallel ratchet is masterworker based. A master process is launched in the DOGMA system which then launches worker tasks on available nodes. Each worker task is simply wrapper code that is used to interact with the newest release version of NONA.
Encapsulated Copper Wire and Copper Mesh Capacitive Sensing for 3-D Printing Applications

Advances in the field of extrusion based 3-D printing have recently allowed the incorporation of embedded electronics and interconnects, in order to increase the functionality of these structures. This paper builds on previous work in the area of fine-pitch copper mesh and embedded copper wire capacitive sensors encapsulated within a 3-D printed structure. Three varieties of sensors were fabricated and tested, including a small area wire sensor (320-μm width), a large area mesh sensor (2 cm2), and a fully embedded demonstration model. In order to test and characterize these sensors, three distinct tests were explored. Specifically, the capacitive sensors were able to distinguish between three metallic materials and distinguish salt water from distilled water. These capacitive sensors have many potential sensing applications, such as biomedical sensing, human interface devices, material sensing, electronics characterization, and environmental sensing. As such, this paper also characterizes the capacitive sensors for an active microfluidic mixer.
The African Rhigonematoidea (Nematoda: Rhigonematida). 2. Six new species of Rhigonema cobb, 1898 (Rhigonematidae)

Six new species of Rhigonema are described from the gut of various African diplopods. Rhigonema fecundum sp. n. , from South Africa, is characterised by medium to fairly long body length, finely pilose anterior region, posterior margin of cephalic collar smoothly fused to body contour, Type 2 genital tract with a long ovejector, presence of a long, closely adpressed, vulval flap, tail shape in both sexes, broad spicules of medium length and complement of 23 copulatory papillae of which three pairs are subdorsal or sublateral in position. Rhigonema oxydesmi sp. n. , from Oxydesmus platycercus concolor, Zaire, is characterised by medium body length, slightly projecting cephalic collar, finely pilose anterior region, Type 2 female genital tract with a long ovejector, presence of a short, adpressed, vulval flap, tail shape in both sexes, medium length spicules with a hamate capitulum and complement of 23 copulatory papillae, three pairs of which are subdorsal or sublateral in position. Rhigonema peziphorum sp. n. , from Sphaerotherium selindum, Zimbabwe, is characterised by medium body length, prominently projecting cephalic collar, finely pilose anterior region, Type 1 female genital tract with a medium length ovejector, rather large eggs, absence of a prominent vulval flap, presence of a spermatophore, tail shape in both sexes, unusually short spicules with a weakly hamate capitulum and complement of 23 copulatory papillae. It is the only known Rhigonema species to form a spermatophore. Rhigonema rostrellum sp. n. , from Ivory Coast, is characterised by medium body length, finely pilose anterior region, Type 2 genital tract with a very long ovejector, presence of a closely adpressed vulval flap, tail shape in both sexes, broad spicules of medium length and complement of 23 copulatory papillae of which three pairs are subdorsal or sublateral in position. Rhigonema spicatum sp. n. , from Congoromus flabellatus, Zaire, is characterised by medium body length, slightly projecting cephalic collar, densely pilose anterior region, Type 2 female genital tract with a long ovejector, presence of an adpressed vulval flap, tail shape in both sexes, relatively short spicules with a hamate capitulum and complement of 23 copulatory papillae. Rhigonema xiphiurus sp. n. , from Oxydesmus sicarius, Zaire, is characterised by medium body length, projecting cephalic collar, coarsely pilose anterior region with bristly microtrichs, microtrichs extending down body to beyond vulval level in female and a similar relative position in the male, Type 2 female genital tract with a long ovejector, elongate female tail, convex conoid male tail with an exceptionally well developed subulate projection, very short spicules and disposition of the 23 copulatory papillae, three pairs of which are dorsal or sublateral in position. A synopsis of the other eight nominal species of African Rhigonema is appended.
Cross-validation of the five-factor interpretive model of the Suicide Opinion Questionnaire.

This study is a cross-validation analysis of the five-factor interpretative model of the Suicide Opinion Questionnaire (Domino, Moore, Westlake, & Gibson, 1982) reported by Rogers and DeShon (1992). Results indicated moderate support for the five-factor model. That is, although the factor analysis results generally supported the 5-factor model, a number of items loaded equally well across 2 or more factors. Additionally, internal consistency and test-retest reliabilities ranged from . 48 to . 85 and from . 34 to . 92, respectively, indicating weaknesses in some of the subscales. Strategies are suggested for the future psychometric development and refinement of the instrument.
Regulation of Fumonisin Biosynthesis in Fusarium verticillioides by a Zinc Binuclear Cluster-Type Gene, ZFR1

ABSTRACT Fusarium verticillioides, a pathogen of maize, produces a class of mycotoxins called fumonisins in infected kernels. In this study, a candidate regulatory gene, ZFR1, was identified in an expressed sequence tag library enriched for transcripts expressed by F. verticillioides during fumonisin B1 (FB1) biosynthesis. ZFR1 deletion mutants exhibited normal growth and development on maize kernels, but fumonisin production was reduced to less than 10% of that of the wild-type strain. ZFR1 encodes a putative protein of 705 amino acids with sequence similarity to the Zn(II)2Cys6 binuclear cluster family that are regulators of both primary and secondary metabolism in fungi. Expression of ZFR1 in colonized germ and degermed kernel tissues correlated with FB1 levels. Overexpression of ZFR1 in zfr1 mutants restored FB1 production to wild-type levels; however, FB1 was not restored in an fcc1 (Fusarium C-type cyclin) mutant by overexpression of ZFR1. The results of this study indicate that ZFR1 is a positive regulator of FB1 biosynthesis in F. verticillioides and suggest that FCC1 is required for ZFR1 function.
A unified energy-based haptic model for a non-rigid object

While we speak of the haptic model, we are still limited to a mass-spring representation or an FEM. This paper proposes a unified model which haptically renders an object without reference to its material property in an energy domain. Furthermore, we develop a 3D mouse type haptic interface prototype for evaluating the proposed method. We first represent a simple 1D object with the proposed method and extend it to 2D deformable object. We experiment with a virtual object of size 20x20 elements to verify that our approach conveys stable haptic sensation to users.
Identification of Steelhead and Resident Rainbow Trout Progeny in the Deschutes River, Oregon, Revealed with Otolith Microchemistry

Abstract Comparisons of strontium:calcium (Sr: Ca) ratios in otolith primordia and freshwater growth regions were used to identify the progeny of steelhead Oncorhynchus mykiss (anadromous rainbow trout) and resident rainbow trout in the Deschutes River, Oregon. We cultured progeny of known adult steelhead and resident rainbow trout to confirm the relationship between Sr:Ca ratios in otolith primordia and the life history of the maternal parent. The mean (±SD) Sr:Ca ratio was significantly higher in the otolith primordia of the progeny of steelhead (0.001461 ± 0.00029; n = 100) than in those of the progeny of resident rainbow trout (0.000829 ± 0.000012; n = 100). We used comparisons of Sr:Ca ratios in the primordia and first-summer growth regions of otoliths to determine the maternal origin of unknown O. mykiss juveniles (n = 272) collected from rearing habitats within the main-stem Deschutes River and tributary rearing habitats and thus to ascertain the relative proportion of each life history morph in ea.
Long-term effect of continuous positive airway pressure in hypertensive patients with sleep apnea.

RATIONALE Continuous positive airway pressure (CPAP) is the current treatment for patients with symptomatic obstructive sleep apnea (OSA). Its use for all subjects with sleep-disordered breathing, regardless of daytime symptoms, is unclear. OBJECTIVES This multicenter controlled trial assesses the effects of 1 year of CPAP treatment on blood pressure (BP) in nonsymptomatic, hypertensive patients with OSA. METHODS We evaluated 359 patients with OSA. Inclusion criteria consisted of an apnea-hypopnea index (AHI) greater than 19 hour(-1), an Epworth Sleepiness Scale score less than 11, and one of the following: under antihypertensive treatment or systolic blood pressure greater than 140 or diastolic blood pressure greater than 90 mm Hg. Patients were randomized to CPAP (n = 178) or to conservative treatment (n = 181). BP was evaluated at baseline and at 3, 6, and 12 months of follow-up. MEASUREMENTS AND MAIN RESULTS Mean (SD) values were as follows: age, 56 +/- 10 years; body mass index (BMI), 32 +/- 5 kg x m(-2); AHI, 45 +/- 20 hour(-1); and Epworth Sleepiness Scale score, 7 +/- 3. After adjusting for follow-up time, baseline blood pressure values, AHI, time with arterial oxygen saturation less than 90%, and BMI, together with the change in BMI at follow-up, CPAP treatment decreased systolic blood pressure by 1.89 mm Hg (95% confidence interval: -3.90, 0.11 mm Hg; P = 0.0654), and diastolic blood pressure by 2.19 mm Hg (95% confidence interval: -3.46, -0.93 mm Hg; P = 0.0008). The most significant reduction in BP was in patients who used CPAP for more than 5.6 hours per night. CPAP compliance was related to AHI and the decrease in Epworth Sleepiness Scale score. CONCLUSIONS In nonsleepy hypertensive patients with OSA, CPAP treatment for 1 year is associated with a small decrease in BP. This effect is evident only in patients who use CPAP for more than 5.6 hours per night. Clinical trial registered with www.clinicaltrials. gov (NCT00127348).
A simple architecture for constant time sorting machines

In this paper, we propose a constant time sorting algorithm on an array composed of comparators and single-pole-double-throw switches, which is far more feasible than other constant time sorting algorithms [21]-[23]. Our results shown that the algorithm uses time <i>T</i> = &Theta;(1) and area <i>A</i> = <i>O</i>(<i>N</i><sup>3</sup>). This nearly matches the <i>AT</i><sup>2</sup> = &Omega;(<i>N</i><sup>2</sup> log<sup>2</sup> <i>N</i>) lower bound for sorting in the VLSI model.
Characterization of the overall and internal dynamics of short oligonucleotides by depolarized dynamic light scattering and NMR relaxation measurements.

The dynamics of three synthetic oligonucleotides d(CG)4, d(CG)6, and d(CGCGTTGTTCGCG) of different length and shape were studied in solution by depolarized dynamic light scattering (DDLS) and time-resolved nuclear Overhauser effect cross-relaxation measurements. For cylindrically symmetric molecules the DDLS spectrum is dominated by the rotation of the main symmetry axis of the cylinder. The experimental correlation times describe the rotation of the oligonucleotides under hydrodynamic stick boundary conditions. It is shown that the hydrodynamic theory of Tirado and Garcia de la Torre gives good predictions of the rotational diffusion coefficients of cylindrically symmetric molecules of the small axial ratios studied here. These relations are used to calculate the solution dimensions of the DNA fragments from measured correlation times. The hydrodynamic diameter of the octamer and dodecamer is 20.5 +/- 1.0 A, assuming a rise per base of 3.4 A. The tridecamer, d(CGCGTTGTTCGCG), adopts a hairpin structure with nearly spherical dimensions and a diameter of 23.0 +/- 2.0 A. The DDLS relaxation measurements provide a powerful method for distinguishing between different conformations of the oligonucleotides (e.g., DNA double-helix versus hairpin structure). Furthermore, the rotational correlation times are a very sensitive probe of the length of different fragments. The NMR results reflect the anisotropic motion of the molecules as well as the amount of local internal motion present. The experimental correlation time from NMR is determined by the rotation of both the short and long axes of the oligonucleotide. (ABSTRACT TRUNCATED AT 250 WORDS)
Bias in the introduction of variation as an orienting factor in evolution

SUMMARY According to New Synthesis doctrine, the direction of evolution is determined by selection and not by “internal causes” that act by way of propensities of variation. This doctrine rests on the theoretical claim that because mutation rates are small in comparison to selection coefficients, mutation is powerless to overcome opposing selection. Using a simple population‐genetic model, this claim is shown to depend on assuming the prior availability of variation, so that mutation may act only as a “pressure” on the frequencies of existing alleles, and not as the evolutionary process that introduces novelty. As shown here, mutational bias in the introduction of novelty can strongly influence the course of evolution, even when mutation rates are small in comparison to selection coefficients. Recognizing this mode of causation provides a distinct mechanistic basis for an “internalist” approach to determining the contribution of mutational and developmental factors to evolutionary phenomena such as homoplasy, parallelism, and directionality.
Molecular insights into the binding selectivity of a synthetic ligand DAAG to Fc fragment of IgG

Affinity chromatography with synthetic ligands has been focused as the potential alternative to protein A‐based chromatography for antibody capture because of its comparable selectivity and efficiency. Better understanding on the molecular interactions between synthetic ligand and antibody is crucial for improving and designing novel ligands. In this work, the molecular interaction mechanism between Fc fragment of IgG and a synthetic ligand (DAAG) was studied with molecular docking and dynamics simulation. The docking results on the consensus binding site (CBS) indicated that DAAG could bind to the CBS with the favorable orientation like a tripod for the top‐ranked binding complexes. The ligand‐Fc fragment complexes were then tested by molecular dynamics simulation at neutral condition (pH 7.0) for 10 ns. The results indicated that the binding of DAAG on the CBS of Fc fragment was achieved by the multimodal interactions, combining the hydrophobic interaction, electrostatic interaction, hydrogen bond, and so on. It was also found that multiple secondary interactions endowed DAAG with an excellent selectivity to Fc fragment. In addition, molecular dynamics simulation conducted at acidic condition (pH 3.0) showed that the departure of DAAG ligand from the surface of Fc fragment was the result of reduced interaction energies. The binding modes between DAAG and CBS not only shed light on the molecular mechanisms of DAAG for antibody purification but also provide useful information for the improvement of ligand design. Copyright © 2014 John Wiley & Sons, Ltd.
Ontology-Mediated Queries

We give solutions to two fundamental computational problems in ontology-based data access with the W3C standard ontology language OWL 2 QL: the succinctness problem for first-order rewritings of ontology-mediated queries (OMQs) and the complexity problem for OMQ answering. We classify OMQs according to the shape of their conjunctive queries (treewidth, the number of leaves) and the existential depth of their ontologies. For each of these classes, we determine the combined complexity of OMQ answering and whether all OMQs in the class have polynomial-size first-order, positive existential, and nonrecursive datalog rewritings. We obtain the succinctness results using hypergraph programs, a new computational model for Boolean functions, which makes it possible to connect the size of OMQ rewritings and circuit complexity.
Bicelle crystallization: a new method for crystallizing membrane proteins yields a monomeric bacteriorhodopsin structure.

Obtaining crystals of membrane proteins that diffract to high resolution remains a major stumbling block in structure determination. Here we present a new method for crystallizing membrane proteins from a bicelle forming lipid/detergent mixture. The method is flexible and simple to use. As a test case, bacteriorhodopsin (bR) from Halobacterium salinarum was crystallized from a bicellar solution, yielding a new bR crystal form. The crystals belong to space group P2(1) with unit cell dimensions of a=45.0 A, b=108.9 A, c=55.9 A, beta=113.58 degrees and a dimeric asymmetric unit. The structure was solved by molecular replacement and refined at 2.0 A resolution. In all previous bR structures the protein is organized as a parallel trimer, but in the crystals grown from bicelles, the individual bR subunits are arranged in an antiparallel fashion.
Improved grid voltage feedforward for strengthening the inverter's adaptability to utility

Grid-connected inverters with the proportional grid voltage feedforward usually achieve satisfied output impedance, which contributes to the low order harmonic elimination. However, a potential positive feedback link is introduced, which decreases the phase margin significantly or even trigger instability when inverters are connected to utility with the non-negligible grid impedance. To maintain the stability and high quality of the injected current for inverters connected to utility with a large set of grid impedance, this study proposes the proportional weighted with partial fundamental grid voltage feedforward. With the aid of the proportional weighted feedforward, the influence of the positive feedback link related to the grid impedance is mitigated. Besides, the steady-state performance is guaranteed by the partial fundamental grid voltage feedforward compensation. Therefore, with the proposed feedforward, the grid-connected inverter can stably operate and achieve high current quality in the weak utility. Then the inverter's adaptability to utility is strengthened. Experiments validate the effectiveness of the proposed method.
Inhibitor of Differentiation 1 Contributes to Head and Neck Squamous Cell Carcinoma Survival via the NF-κB/Survivin and Phosphoinositide 3-Kinase/Akt Signaling Pathways

Purpose: A key issue in cancer is apoptosis resistance. However, little is known about the transcription factors that contribute to cellular survival of head and neck squamous cell carcinoma (HNSCC). Experimental Design: Three batches (54, 64, and 38) of HNSCC specimens were used for cellular and molecular analyses to determine the major molecular signaling pathways for cellular survival in HNSCC. Animal models (cell culture and xenografts) were used to verify the importance of apoptosis resistance in HNSCC. Results: Inhibitor of differentiation (Id) family member, Id1, was significantly upregulated in clinical HNSCC specimens and acted to protect keratinocytes from apoptosis. Transfection of HNSCC cells with Id1 in vitro induced the phosphorylation of Akt (p-Akt) via phosphoinositide 3-kinase and increased the expression of survivin via NF-κB. Blockage of both pathways by specific inhibitors (LY294002 and IκBαM, respectively) abrogated Id1-induced cell survival of keratinocytes. In vivo studies showed that increased expression of Id1 allowed nontumorigenic keratinocytes (Rhek-1A) to become tumorigenic in nude mice by increased expression of survival genes such as p-Akt and survivin. More importantly, short interfering RNA for Id1 significantly reduced HNSCC tumor volume of HNSCC in xenograft studies. Analysis of clinical data verified the importance of the Id1 downstream molecule, survivin, in the prognosis of HNSCC patients. Conclusions: The above data, taken together, suggest that Id1 and its downstream effectors are potential targets for treatment of HNSCC because of their contribution to apoptosis resistance. Clin Cancer Res; 16(1); 77–87
Unexploited Acacia cyanophylla seeds: potential food sources of ω6 fatty acids and antioxidants?

BACKGROUND In order to investigate new sources of dietary phytochemicals, recent studies have focused on underexploited seeds. In this study the total lipid contents, fatty acid profiles and levels of soluble proteins, minerals and antioxidants in seeds from 12 Acacia cyanophylla ecotypes commonly grown in Tunisia were determined. RESULTS Total lipids averaged 101.7 g kg(-1) on a dry weight basis. Linoleic (61.11-65.45% of total fatty acid content), oleic (19.67-22.85%) and palmitic (9.18-9.98%) acids were the principal fatty acids. Smaller proportions of stearic (1.49-1.82%), vaccenic (1.13-2.05%) and palmitoleic (0.34-0.58%) acids were also quantified. Proteins (by Kjeldahl assay) averaged 107.2 g kg(-1) on a dry weight basis. Total phenolics averaged 1.91 g gallic acid equivalent kg(-1) dry weight (DW) and total flavonoids averaged 0.40 g rutin equivalent kg(-1) DW. The free radical-scavenging activity determined by 2,2-diphenyl-1-picrylhydrazyl assay averaged 0.59 mmol L(-1) Trolox equivalent antioxidant capacity (TEAC), while that determined by 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) assay averaged 0.28 mmol L(-1) TEAC. CONCLUSION The findings of this study confirm the presence of ω6 fatty acids at high levels in A. cyanophylla seeds. These metabolites could be used as such and/or extracted for the formulation of supplements and/or ingredients to provide a ratio close to the ideal for the ω3/ω6 balance.