Miracle-dz/UniFAR-FTUs huggingface dataset:
A DnaK Homolog in Myxococcus xanthus Is Involved in Social Motility and Fruiting Body Formation

ABSTRACT Myxococcus xanthus is a gram-negative soil bacterium which exhibits a complex life cycle and social behavior. In this study, two developmental mutants of M. xanthus were isolated through Tn5 transposon mutagenesis. The mutants were found to be defective in cellular aggregation as well as in sporulation. Further phenotypic characterization indicated that the mutants were defective in social motility but normal in directed cell movements. Both mutations were cloned by a transposon-tagging method. Sequence analysis indicated that both insertions occurred in the same gene, which encodes a homolog of DnaK. Unlike the dnaK genes in other bacteria, this M. xanthus homolog appears not to be regulated by temperature or heat shock and is constitutively expressed during vegetative growth and under starvation. The defects of the mutants indicate that this DnaK homolog is important for the social motility and development of M. xanthus.
Case Study: Modeling the Lateral Mobility of the Rio Grande below Cochiti Dam, New Mexico

The Cochiti reach of the Rio Grande served as a case study to test the hypothesis that the lateral mobility of an alluvial river decreases as the river approaches equilibrium. The lateral mobility of the river was measured using a geographic information system from digitized aerial photographs of the nonvegetated active channel between 1918 and 2001. Reach-averaged lateral mobility was quantified in terms of width change, lateral migration, and total lateral movement. By 2001, the width of the Cochiti Reach was close to the expected equilibrium width indicating that the river had adjusted to the incoming water and sediment load. An exponential equation based on deviation from equilibrium width described 95–96% of the variance in channel width, 78–90% of variance in migration rates, and 92% of the variance in total lateral movement between 1918 and 1992. For validation of the model, the 2001 width and migration rates were predicted with errors as low as 19 and 8%, respectively. The exponential width model .
Functional consequences of tooth design: effects of blade shape on energetics of cutting

SUMMARY Dental structures capture, retain and fragment food for ingestion. Gnathostome dentition should be viewed in the context of the prey's material properties. Animal muscle and skin are mechanically tough materials that resist fragmentation unless energy is continually supplied directly to the tip of the fracture by some device such as a blade edge. Despite the variety of bladed tooth morphologies in gnathostomes, few studies have experimentally examined the effects of different blade designs on cutting efficiency. We tested the effects of blades with and without contained notches and in a `fang' configuration on the force and energy required to fracture raw, unprocessed biological tissues (fish and shrimp) using a double guillotine device. Blade design strongly affects the work required to fragment biological tissues. A notched blade reduced the work to fracture of tissues tested by up to 600 J m–2 (50% reduction). The specific angle of the notch had a significant effect, with acute angles more effectively reducing work to fracture. A bladed triangle matched to a notch reduced work to fracture more than a notch–straight blade pair. Strain patterns seen while cutting photoelastic gelatin indicate that the reduction in work to fracture with triangular and notched blades arises from a combination of `trapping ability' and blade approach angle causing the material to fracture at lower overall strain levels. These results show that the notched blade designs found in a wide variety of vertebrate dentitions reduce the energy expenditure (and presumably handling time) when cutting tough prey materials like animal flesh.
Simulating Effect of Channel Changes on Stream Infiltration

We use a saturated‐unsaturated flow model (UNSAT2) to study the effect of soil cementing and channel widening on infiltration and recharge in two idealized profiles along the Rillito River of southern Arizona. The channel sections associated with the profiles are 202‐ft (61.6‐m) and 326‐ft (99.4‐m) wide. A synthetic 10‐yr runoff in the river provides head values for generating infiltration before and after bank protection in these two sections. Results from the two base simulations are combined to produce four additional cases. Soil cementing the banks of the river without widening the channel reduces infiltration and recharge by 15% for the 326‐ft wide (99.4‐m) channel and by 25% for the 202‐ft wide (61.6‐m) channel. Increasing channel width together with bank protection increases infiltration 25% for our two sections. Increasing channel width without bank protection, however, increases infiltration by 46% for our conditions. Channel narrowing with bank protection markedly increases infiltration rates, a.
Combining Distant and Partial Supervision for Relation Extraction

Broad-coverage relation extraction either requires expensive supervised training data, or suffers from drawbacks inherent to distant supervision. We present an approach for providing partial supervision to a distantly supervised relation extractor using a small number of carefully selected examples. We compare against established active learning criteria and propose a novel criterion to sample examples which are both uncertain and representative. In this way, we combine the benefits of fine-grained supervision for difficult examples with the coverage of a large distantly supervised corpus. Our approach gives a substantial increase of 3.9% endto-end F1 on the 2013 KBP Slot Filling evaluation, yielding a net F1 of 37.7%.
Particle Filtering for PLCA model with Application to Music Transcription

Automatic Music Transcription (AMT) consists in automatically estimating the notes in an audio recording, through three attributes: onset time, duration and pitch. Probabilistic Latent Component Analysis (PLCA) has become very popular for this task. PLCA is a spectrogram factorization method, able to model a magnitude spectrogram as a linear combination of spectral vectors from a dictionary. Such methods use the Expectation-Maximization (EM) algorithm to estimate the parameters of the acoustic model. This algorithm presents well-known inherent defaults (local convergence, initialization dependency), making EM-based systems limited in their applications to AMT, particularly in regards to the mathematical form and number of priors. To overcome such limits, we propose in this paper to employ a different estimation framework based on Particle Filtering (PF), which consists in sampling the posterior distribution over larger parameter ranges. This framework proves to be more robust in parameter estimation, more flexible and unifying in the integration of prior knowledge in the system. Note-level transcription accuracies of 61.8 $\%$ and 59.5 $\%$ were achieved on evaluation sound datasets of two different instrument repertoires, including the classical piano (from MAPS dataset) and the marovany zither, and direct comparisons to previous PLCA-based approaches are provided. Steps for further development are also outlined.
The thermal history of the New York basement determined from 40Ar/39Ar K‐feldspar studies

Constraints on the thermochronologic evolution of the New York crystalline basement are mainly restricted to the high-temperature early cooling history following 1.1 Ga Grenville metamorphism (U-Pb methods) and the late cooling history (fission track methods). The thermal history for the ∼one billion years between these intervals is herein assessed using 40Ar/39Ar hornblende, muscovite, biotite and K-feldspar thermochronology. Hornblende preferred ages suggest cooling below ∼450–500°C between ca. 900 and 950 Ma. Total gas ages of biotites range from ∼746–1060 Ma, and their age spectra complexity is probably related to younger thermal events and/or excess argon. A single muscovite analysis yields a preferred age of 854 Ma. Argon isotope analyses of K-feldspar provide a quantitative evaluation of the thermal history between ∼175 and 350°C. Multi-diffusion domain thermochronology on highly variable K-feldspar results yield internally consistent thermal histories and, along with geologic constraints, suggest thermal maxima of 275–350°C at ca. 700, 470–450 and 300 Ma. Combining all of the K-feldspar analyses provides an internally consistent thermal history for the region and allows for the following inferences. Reheating at ∼700 Ma associated with Late Precambrian rifting during the formation of the Iapetus ocean apparently affected the entire Adirondack region with the highest temperatures occurring in the eastern part of New York. Local reheating in the Ordovician is inferred to have affected the eastern Adirondack Mountains and probably resulted from the combined effects of burial during the Early Paleozoic, emplacement of Taconic thrust sheets and migration of hot fluids along normal faults during the Taconic orogeny. High paleotemperatures for the Devonian section of eastern New York are related to maximum burial of the basement during the Carboniferous at ca. 300 Ma.
Automatic segmentation of Chinese Mandarin speech into syllable-like

In this paper, we propose a novel approach to automatically segment a continuous Mandarin speech into syllable-like units. The main idea of our algorithm is to merge two round distinct selected boundaries using feature information generated from time and frequency domain. The first round segmentation is mainly based on aggregating the characteristics of different frequency regions and the second round employees zero crossing rate to improve the accuracy of segment results. The experimental results indicate that our hybrid method has high accuracy and coverage with respect to the reference boundaries even in low error tolerance.
Predicting the Quality of User Experiences to Improve Productivity and Wellness

College students often struggle to balance their work with personal wellness. In part, this occurs because students work when they are unable to focus. We hypothesize that we can adapt the Experience Sampling Method (ESM) to build a model of users’ efficacy and predict when they will be most likely to experience flow, a state of motivation and immersion. We also hypothesize that we can present this information effectively to users, allowing them to understand when they are most likely to achieve flow. In order to test these hypotheses, we introduce the Productivity and Wellness Pal (PaWPal), a smartphone-based application that seeks to make users aware of their efficacy at various tasks as well as which courses of action are likely to lead to immersive experiences.
Selective killing of breast cancer cells expressing activated CD44 using CD44 ligand-coated nanoparticles in vitro and in vivo

The cell surface glycoprotein CD44 is expressed in cancer cells and has been used as a therapeutic target in preclinical studies. However, the ubiquitous expression of CD44 in numerous cell types, including hematopoietic cells, has hindered its application in targeted therapy. Here, we demonstrated that CD44 was activated on breast cancer cells but was inactive on normal cells in vitro and in vivo. We analyzed 34 clinical primary tumor and normal breast tissues and demonstrated that CD44 was in an active state on breast cancer cells but in an inactive state on normal cells. Furthermore, based on the binding property of CD44 with its ligand hyaluronan (HA), we self-assembled HA-coated nanoparticles and studied their selective targeting efficacy. Our results indicate that HA-coated nanoparticles bearing the CD44 ligand selectively targeted cancer cells both in vitro and in vivo, killing breast cancer cells while sparing normal cells. Our study suggested that the active state of CD44 plays a crucial role in the selective targeting of breast cancer cells by avoiding nonspecific toxicity to CD44-quiescent normal cells. These findings may provide a new idea for the selective targeting of cancer cells in other human cancers.
Suppression of alcohol intake after administration of the Chinese herbal medicine, NPI-028, and its derivatives.

The Chinese herbal medicine, NPI-028, has been used for centuries in China to counteract alcohol intoxication. The present study used a number of different experimental conditions to determine whether NPI-028 and its derivatives might selectively influence alcohol intake in rodents that naturally exhibit high alcohol intakes. It was determined that intraperitoneal (i.p.) injections of NPI-028 (0.5, 0.75, and 1.0 g/kg) suppressed alcohol intake by up to 30% in both alcohol-preferring P and Fawn-Hooded (FH) rats during a continuous access schedule. These injections did not significantly affect food or water intakes, nor did the highest dose of NPI-028 (1 g/kg) alter blood ethanol levels after an i.p. injection of 2.5 g/kg of ethanol. In P rats, it was found that NPI-028 was orally active with the dose of 1.5 g/kg having a greater effect on ethanol intake than the 1.0 g/kg dose; once again, food and water intakes were not significantly altered. In FH rats maintained on a limited access schedule (1 hr/day), alcohol intake was completely abolished by 1.5 g/kg of NPI-028. Chronic i.p. administration of NPI-028 (0.75 g/kg) for four consecutive days in FH rats maintained on a continuous access schedule did not lead to any diminution of its alcohol-suppressant effects. Thus, NPI-028 has significant effects on alcohol intake without much effect on water and food intake, and tolerance does not readily develop to these effects. The i.p. administration of a partially purified extract (NPI-031) of NPI-028, obtained by countercurrent chromatography, also dose-dependently suppressed ethanol intake in FH rats, but the highest dose 200 mg/kg) also significantly decreased food intake. Finally, the i.p. administration of puerarin (NPI-31G), an isoflavone isolated from NPI-031 by countercurrent chromatography, significantly reduced ethanol intake in FH rats without affecting food or water intake. Therefore, NPI-028 and one of its pure components, NPI-031G, selectively reduced ethanol intake in alcohol-preferring rats.
An asymptotic numerical method for inverse elastic shape design

Inverse shape design for elastic objects greatly eases the design efforts by letting users focus on desired target shapes without thinking about elastic deformations. Solving this problem using classic iterative methods (e.g., Newton-Raphson methods), however, often suffers from slow convergence toward a desired solution. In this paper, we propose an asymptotic numerical method that exploits the underlying mathematical structure of specific nonlinear material models, and thus runs orders of magnitude faster than traditional Newton-type methods. We apply this method to compute rest shapes for elastic fabrication, where the rest shape of an elastic object is computed such that after physical fabrication the real object deforms into a desired shape. We illustrate the performance and robustness of our method through a series of elastic fabrication experiments.
Dirichlet Process Mixture Models : Application to Brain Image Segmentation

The ability of nonparametric models to automatically adapt to the complexity of data makes them particularly suitable for neuroimaging applications, where it is often preferable to avoid assumptions on the correct model structure. We have applied a multivariate Dirichlet process Gaussian mixture model (DPGMM) for segmenting main cerebral tissues (grey matter, white matter and cerebrospinal fluid) by learning from multiple MRI modalities (T1, T2 and PD). We experimentally show that a multivariate DPGMM produced significantly more consistent and accurate segmentations than an equivalent univariate DPGMM trained on a single modality (T1). This is also the first known attempt at performing lesion segmentation with DP mixture models. Our preliminary results show great promise, as the DPGMMs were able to correctly identify most traumatic brain injury lesions in a multimodal MRI dataset (MPRAGE, FLAIR, GE, T2 and PD) and have demonstrated their capability to learn intricate multidimensional probability distributions.
SDA*: A Simple and Unifying Solution to Recent Bioinformatic Challenges for Conservation Genetics

Recently, several algorithms have been proposed to tackle different conservation questions under phylogenetic diversity. Such questions are variants of the more general problem of budgeted reserve selection under split diversity, an NP-hard problem. Here, we present a novel framework, Split Diversity Algorithm* (SDA*), to unify all these attempts. More specifically, SDA* transforms the budgeted reserve selection problem into a binary linear programming(BLP), that can be solved by available linear optimization techniques. SDA* guarantees to find optimal solutions in reasonable time.
A Computational Approach for Deciphering the Organization of Glycosaminoglycans

Background Increasing evidence has revealed important roles for complex glycans as mediators of normal and pathological processes. Glycosaminoglycans are a class of glycans that bind and regulate the function of a wide array of proteins at the cell-extracellular matrix interface. The specific sequence and chemical organization of these polymers likely define function; however, identification of the structure-function relationships of glycosaminoglycans has been met with challenges associated with the unique level of complexity and the nontemplate-driven biosynthesis of these biopolymers. Methodology/Principal Findings To address these challenges, we have devised a computational approach to predict fine structure and patterns of domain organization of the specific glycosaminoglycan, heparan sulfate (HS). Using chemical composition data obtained after complete and partial digestion of mixtures of HS chains with specific degradative enzymes, the computational analysis produces populations of theoretical HS chains with structures that meet both biosynthesis and enzyme degradation rules. The model performs these operations through a modular format consisting of input/output sections and three routines called chainmaker, chainbreaker, and chainsorter. We applied this methodology to analyze HS preparations isolated from pulmonary fibroblasts and epithelial cells. Significant differences in the general organization of these two HS preparations were observed, with HS from epithelial cells having a greater frequency of highly sulfated domains. Epithelial HS also showed a higher density of specific HS domains that have been associated with inhibition of neutrophil elastase. Experimental analysis of elastase inhibition was consistent with the model predictions and demonstrated that HS from epithelial cells had greater inhibitory activity than HS from fibroblasts. Conclusions/Significance This model establishes the conceptual framework for a new class of computational tools to use to assess patterns of domain organization within glycosaminoglycans. These tools will provide a means to consider high-level chain organization in deciphering the structure-function relationships of polysaccharides in biology.
Optical Dating of Tsunami-Laid Sands

The ages of some tsunami deposits can be determined by optical dating, a key requirement being that the deposits are derived from sediment that was reworked and exposed to daylight by tidal currents, waves, wind, or bioturbation during the last years before the tsunami. Measurements have been made using 1.4 eV (infrared) excitation of K-feldspar grains separated from samples of prehistoric tsunami sand sheets and modern analogs of tsunami source sediments at four sites in Washington state and British Columbia. Source sands gave equivalent doses indicative of recent exposure to daylight. Tsunami sand at Cultus Bay, Washington, yielded an optical age of 1285 ± 95 yr (calendric years before A.D. 1995, ±1σ). At 2σ, this age overlaps the range of from 1030 to 1100 yr determined through a combination of high-precision radiocarbon dating and stratigraphic correlation. Tsunami sands at three sites near Tofino and Port Alberni on Vancouver Island, British Columbia, have optical ages of 260 ± 20, 325 ± 25, and 335 ± 45 yr. Historical records and radiocarbon dating show that the sand at each of the three sites is between 150 and 400 yr old. These optical ages support the hypothesis that the Vancouver Island sands were deposited by a tsunami generated by a large earthquake on the Cascadia subduction zone about 300 yr ago.
Investigating Temporal and Spatial Trends of Brand Images Using Twitter Opinion Mining

The growing popularity of social network services has led to many studies of various phenomena in this area. However, most of this research has been conducted using English language data, and relatively little has considered Korean. In this paper, we demonstrate a systematic analysis framework using Korean Twitter data to mine temporal and spatial trends of brand images. A publicly available Korean morpheme analyzer is used to analyze Korean tweets grammatically, and we construct Korean polarity dictionaries containing a noun, adjective, verb, and/or root to automatically analyze the sentiment of each tweet message. Sentiment classification is performed by a support vector machine and multinomial naïve Bayes classifier. In particular, our own feature selection step improves the support vector machine sentiment classification accuracy to 80%. Based on this result, we visualize the temporal and spatial distribution of brand images, and present the temporal changes of brand-related keyword networks. Our analysis enables trends in brand awareness to be systematically traced and evaluated. This allows various other analyses, such as advantages and disadvantages of the brand, and a comparison with its competitors.
Information Bottleneck on General Alphabets

We prove rigorously a source coding theorem that can probably be considered folklore, a generalization to arbitrary alphabets of a problem motivated by the Information Bottleneck method. For general random variables (Y, X), we show essentially that for some <tex>$n\in \mathbb{N}$</tex>, a function <tex>$f$</tex> with rate limit <tex>$\log\vert f\vert \leq nR$</tex> and <tex>$I(\mathsf{Y}^{n};f(\mathsf{X}^{n}))\geq n\mathcal{S}$</tex> exists if and only if there is a random variable <tex>$\mathsf{U}$</tex> such that the Markov chain <tex>$\mathsf{Y}\circ\! \! \! \! \! {-}\mathsf{X}\circ\! \! \! \! \! {-}\mathsf{U}$</tex> holds, <tex>$I\mathsf{(U;X)}\leq R$</tex> and <tex>$I\mathsf{(U;Y)}\geq \mathcal{S}$</tex>. The proof relies on the well established discrete case and showcases a technique for lifting discrete coding theorems to arbitrary alphabets.