Miracle-dz/UniFAR-FTUs huggingface dataset:
Transformation of structured documents

SUMMARY Many documents have a definable structure. Some document formatting systems, like the LaTeX formatter, use a structural notation. In recent years the general mark-up language SGML has gained popularity. In this work we study the transformation of a structure to another. For example, technical journals have their structure definitions, and an article originally written for one journal must be restructured before it can be submitted to another journal. We assume that structure definitions are grammatical, and study what kind of transformations can be automatized or at least semiautomatized. We took a collection of computer science journals and compared their structure definitions. We classified differences as simple, local and global. As transformation techniques we studied syntax directed translation schemata and tree transducers. Our conclusion was that simple and local transformations can be automatized or semiautomatized, depending whether additional information is not needed, while global transformations are difficult to automatize. Transformations were tested in our prototype syntax-directed document processing system. The system has one module for editing a document under one structure definition, and another module for changing a document from one structure definition to another.
Arabidopsis Tic110 Is Essential for the Assembly and Function of the Protein Import Machinery of Plastidsw⃞

The translocon at the inner envelope membrane of chloroplasts (Tic) plays a central role in plastid biogenesis by coordinating the sorting of nucleus-encoded preproteins across the inner membrane and coordinating the interactions of preproteins with the processing and folding machineries of the stroma. Despite these activities, the precise roles of known Tic proteins in translocation, sorting, and preprotein maturation have not been defined. In this report, we examine the in vivo function of a major Tic component, Tic110. We demonstrate that Arabidopsis thaliana Tic110 (atTic110) is essential for plastid biogenesis and plant viability. The downregulation of atTic110 expression results in the reduced accumulation of a wide variety of plastid proteins. The expression of dominant negative mutants of atTic110 disrupts assembly of Tic complexes and the translocation of preproteins across the inner envelope membrane. Together, these data suggest that Tic110 plays a general role in the import of nuclear-encoded preproteins as a common component of Tic complexes.
Native language detection with 'cheap' learner corpora

We begin by showing that the best publicly available, multiple-L1 learner corpus, the International Corpus of Learner English (Granger et al. 2009), has issues when used directly for the task of native language detection (NLD). The topic biases in the corpus are a confounding factor that results in cross-validated performance that appears misleadingly high, for all the feature types which are traditionally used. Our approach here is to look for other, cheap ways to get training data for NLD. To that end, we present the web-scraped Lang-8 learner corpus, and show that it is useful for the task, particularly if large quantities of data are used. This also seems to facilitate the use of lexical features, which have been previously avoided. We also investigate ways to do NLD that do not involve having learner corpora at all, including double-translation and extracting information from L1 corpora directly. All of these avenues are shown to be promising.
Numerical simulation of red blood cells' deformation using SPH method

A numerical simulation method for the Red Blood Cells’ (RBC) deformation is presented in this study. The two-dimensional RBC membrane is modeled by the spring network, where the elastic stretch/compression energy and the bending energy are considered with the constraint of constant RBC surface area. Smoothed Particle Hydrodynamics (SPH) method is used to solve the NavierStokes equation coupled with the Plasma-RBC membrane and Cytoplasm- RBC membrane interaction. To verify the method, the motion of a single RBC is simulated in Poiseuille flow and compared with the results reported earlier. Typical motion and deformation mechanism of the RBC is observed.
Individual Differential Privacy: A Utility-Preserving Formulation of Differential Privacy Guarantees

Differential privacy is a popular privacy model within the research community because of the strong privacy guarantee it offers, namely that the presence or absence of any individual in a data set does not significantly influence the results of analyses on the data set. However, enforcing this strict guarantee in practice significantly distorts data and/or limits data uses, thus diminishing the analytical utility of the differentially private results. In an attempt to address this shortcoming, several relaxations of differential privacy have been proposed that trade off privacy guarantees for improved data utility. In this paper, we argue that the standard formalization of differential privacy is stricter than required by the intuitive privacy guarantee it seeks. In particular, the standard formalization requires indistinguishability of results between any pair of neighbor data sets, while indistinguishability between the actual data set and its neighbor data sets should be enough. This limits the data controller’s ability to adjust the level of protection to the actual data, hence resulting in significant accuracy loss. In this respect, we propose individual differential privacy, an alternative differential privacy notion that offers the same privacy guarantees as standard differential privacy to individuals (even though not to groups of individuals). This new notion allows the data controller to adjust the distortion to the actual data set, which results in less distortion and more analytical accuracy. We propose several mechanisms to attain individual differential privacy and we compare the new notion against standard differential privacy in terms of the accuracy of the analytical results.
SOX9, a potential tumor suppressor in cervical cancer, transactivates p21WAF1/CIP1 and suppresses cervical tumor growth

Sex-determining region Y-box 9 protein (SOX9) is a transcription factor that may act as both oncogene and tumor suppressor depending on tumor origin. Here we found that SOX9 expression was progressively decreased in cervical carcinoma in situ and especially in invasive cervical carcinoma, compared with normal cervix tissue. The effects of SOX9 on the proliferation, viability, and tumor formation of cervical carcinoma cells were assessed through the silencing and overexpression of SOX9. Overexpression of SOX9 in cervical carcinoma cells (SiHa and C33A) inhibited cell growth in vitro and tumor formation in vivo. In agreement, the silencing of SOX9 in HeLa cells promoted cell growth in culture and tumor formation in mice. Overexpression of SOX9 transactivated p21WAF1/CIP1 via a specific promoter region, thus blocking G1/S transition. The quantitative chromatin immunoprecipitation analysis revealed physical interaction between SOX9 and the specific region of the p21WAF1/CIP1 promoter. We suggest that SOX9 is a potential therapeutic target in cervical carcinoma, that specifically transactivates p21WAF1/CIP1.
Spatiotemporal Patterns of Host-Seeking Ixodes scapularis Nymphs (Acari: Ixodidae) in the United States

Abstract The risk of Lyme disease for humans in the eastern United States is dependent on the density of host-seeking Ixodes scapularis Say nymphal stage ticks infected with Borrelia burgdorferi. Although many local and regional studies have estimated Lyme disease risk using these parameters, this is the first large-scale study using a standardized methodology. Density of host-seeking I. scapularis nymphs was measured by drag sampling of closed canopy deciduous forest habitats in 95 locations spaced among 2° quadrants covering the entire United States east of the 100th meridian. Sampling was done in five standardized transects at each site and repeated three to six times during the summer of 2004. The total number of adults and nymphs of the seven tick species collected was 17,972, with 1,405 nymphal I. scapularis collected in 31 of the 95 sites. Peak global spatial autocorrelation values were found at the smallest lag distance (300 km) and decreased significantly after 1,000 km. Local autocorrelation statistics identified two significant high-density clusters around endemic areas in the northeast and upper Midwest and a low-density cluster in sites south of the 39th parallel, where only 21 nymphs were collected. Peak nymphal host-seeking density occurred earlier in the southern than in the most northern sites. Spatiotemporal density patterns will be combined with Borrelia prevalence data as part of a 4-yr survey to generate a nationwide spatial risk model for I. scapularis-borne Borrelia, which will improve targeting of disease prevention efforts.
Home fortification with calcium reduces Hb response to iron among anaemic Bangladeshi infants consuming a new multi-micronutrient powder formulation

Abstract Objective To investigate whether the recommended dietary intake of Ca in anaemic infants compromises the expected Hb response, via home fortification with a new Ca- and Fe-containing Sprinkles™ micronutrient powder (MNP). Design A double-blind, randomized controlled, 2-month trial was conducted in Bangladesh. Infants were randomized to one of two MNP intervention groups containing Fe and other micronutrients, with or without Ca. Hb, anthropometrics and dietary intake were measured pre- and post-intervention while family demographics were collected at baseline. Setting Twenty-six rural villages in the Kaliganj sub-district of Gazipur, Bangladesh. Subjects One hundred infants aged 6–11 months. Results A significant increase in Hb (MNP, 13·3 (sd 12·6) g/l v. Ca-MNP, 7·6 (sd 11·6) g/l; P < 0·0001) was noted in infants from both groups. However, infants receiving MNP without Ca had a significantly higher end-point Hb concentration (P = 0·024) and rate of anaemia recovery (P = 0·008). Infants receiving MNP with Ca were more likely to remain anaemic (OR 3·2; 95 % CI 1·4, 7·5). Groups did not differ in dietary intake or demographic and anthropometric indicators. Conclusions Although both groups showed significant improvement in Hb status, the nutrient–nutrient interaction between Fe and Ca may have diminished the Hb response in infants receiving the Ca-containing MNP.
Effect of Calcium on Force‐Velocity‐Length Relations of Heart Muscle of the Cat

The influence of calcium concentration in the bathing solution on the force-velocity relations of the isolated, electrically excited cat papillary muscle was examined. Shortening velocity was directly measured at minimum loads by unloading or load clamping the muscle from the preload (at the length, Lmax, where maximum active tensio was developed) to 0 (zero-load clamp), 2, 5, 10, and 15% of the total tension, P0. All measurements were made in the physiological length range between Lmax and 12.5% below Lmax. Increasing the calcium concentration augmented the measured maximum unloaded shortening velocity and shifted the normalized force-velocity relation when force was expressed as a fraction of P0. These observations suggest that the activating calcium has an action more complex than the binding to troponin alone.
Site-Directed Spin-Labeling Analysis of Reconstituted Mscl in the Closed State

The mechanosensitive channel from Escherichia coli (Eco-MscL) responds to membrane lateral tension by opening a large, water-filled pore that serves as an osmotic safety valve. In an attempt to understand the structural dynamics of MscL in the closed state and under physiological conditions, we have performed a systematic site-directed spin labeling study of this channel reconstituted in a membrane bilayer. Structural information was derived from an analysis of probe mobility, residue accessibility to O2 or NiEdda and overall intersubunit proximity. For the majority of the residues studied, mobility and accessibility data showed a remarkable agreement with the Mycobacterium tuberculosis crystal structure, clearly identifying residues facing the large water-filled vestibule at the extracellular face of the molecule, the narrowest point along the permeation pathway (residues 21–26 of Eco-MscL), and the lipid-exposed residues in the peripheral transmembrane segments (TM2). Overall, the present dataset demonstrates that the transmembrane regions of the MscL crystal structure (obtained in detergent and at low pH) are, in general, an accurate representation of its structure in a membrane bilayer under physiological conditions. However, significant differences between the EPR data and the crystal structure were found toward the COOH-terminal end of TM2.
Interplay between Exonic Splicing Enhancers, mRNA Processing, and mRNA Surveillance in the Dystrophic Mdx Mouse

Background Pre-mRNA splicing, the removal of introns from RNA, takes place within the spliceosome, a macromolecular complex composed of five small nuclear RNAs and a large number of associated proteins. Spliceosome assembly is modulated by the 5′ and 3′ splice site consensus sequences situated at the ends of each intron, as well as by exonic and intronic splicing enhancers/silencers recognized by SR and hnRNP proteins. Nonsense mutations introducing a premature termination codon (PTC) often result in the activation of cellular quality control systems that reduce mRNA levels or alter the mRNA splicing pattern. The mdx mouse, a commonly used genetic model for Duchenne muscular dystrophy (DMD), lacks dystrophin by virtue of a premature termination codon (PTC) in exon 23 that also severely reduces the level of dystrophin mRNA. However, the effect of the mutation on dystrophin RNA processing has not yet been described. Methodology/Principal Finding Using combinations of different biochemical and cellular assays, we found that the mdx mutation partially disrupts a multisite exonic splicing enhancer (ESE) that is recognized by a 40 kDa SR protein. In spite of the presence of an inefficient intron 22 3′ splice site containing the rare GAG triplet, the mdx mutation does not activate nonsense-associated altered splicing (NAS), but induces exclusively nonsense-mediated mRNA decay (NMD). Functional binding sites for SR proteins were also identified in exon 22 and 24, and in vitro experiments show that SR proteins can mediate direct association between exon 22, 23, and 24. Conclusions/Significance Our findings highlight the complex crosstalk between trans-acting factors, cis-elements and the RNA surveillance machinery occurring during dystrophin mRNA processing. Moreover, they suggest that dystrophin exon–exon interactions could play an important role in preventing mdx exon 23 skipping, as well as in facilitating the pairing of committed splice sites.
Let technology do the work: Improving prediction of massive transfusion with the aid of a smartphone application

BACKGROUND The use of massive transfusion protocols (MTPs) is now common in civilian trauma settings, and early activation of MTP has been shown to increase survival of MTP recipients. Numerous MTP prediction tools have been developed; however, they are often cumbersome to use efficiently or have traded predictive power for ease of use. We hypothesized that a highly accurate predictor of massive transfusion could be created and incorporated into a smartphone application that would provide an additional tool for clinicians to use in directing the resuscitation of critically injured patients. METHODS Data from all trauma admissions since the inception of MTP were put in place at Grady Memorial Hospital in Atlanta, Georgia, were collected. A predictive model was developed using the least absolute shrinkage and selection operator (LASSO) and 10-fold cross validation. Data were resampled over 500 iterations, each using a unique and random subset of 80% of the data for model training and 20% for validation. RESULTS The trauma registry contained 13,961 cases between 2007 and November 2011, of which 10,900 were complete and 394 received MTP. Of 44 input terms, only the mechanism of injury, heart rate, systolic blood pressure, and base deficit were found to be important predictors of massive transfusion. Our model has an area under the receiver operating curve of 0.96 (against data not used during model training) and accurately predicted MTP status for 97% of all patients. The model accurately discriminated full MTPs from MTP activations that did not meet criteria for massive transfusion. While complex to calculate by hand, our model has been packaged into a mobile application, allowing for efficient use while minimizing potential for user error. CONCLUSION We have developed a highly accurate model for the prediction of massive transfusion that has potential to be easily accessed and used within a simple and efficient mobile application for smartphones. LEVEL OF EVIDENCE Prognostic/epidemiologic study, level III.
Continuum Arm Robotic Manipulator: A Review

Traditional robots have rigid underlying structures that limit their ability to interact with their environment. For example, conventional robot manipulators have rigid links and can manipulate objects using only their specialised end effectors. These robots often encounter difficulties operating in unstructured and highly congested environments. A variety of animals and plants exhibit complex movement with soft structures devoid of rigid components. In this paper survey of literature related to continuum arm of robotic manipulator based on biological inspiration is carried out. It defines the fundamental difference between discrete, serpentine and continuum robot devices; presents the 'state of the art' of continuum robots and outlines their areas of application; and introduces some control issues. Finally some conclusions regarding the continued development of these devices are made.
Genome Sequence of Dyella ginsengisoli Strain LA-4, an Efficient Degrader of Aromatic Compounds

ABSTRACT Dyella ginsengisoli strain LA-4 can efficiently degrade environmental pollutants such as biphenyl and azo dyes. Here, we present a 4.55-Mb draft genome sequence of strain LA-4, which may provide further insights into the molecular mechanism in environmental pollution remediation.
A construction of a space-time code based on number theory

We construct a full data rate space-time (ST) block code over M=2 transmit antennas and T=2 symbol periods, and we prove that it achieves a transmit diversity of 2 over all constellations carved from Z[i]/sup 4/. Further, we optimize the coding gain of the proposed code and then compare it to the Alamouti code. It is shown that the new code outperforms the Alamouti (see IEEE J Select. Areas Commun., vol.16, p.1451-58, 1998) code at low and high signal-to-noise ratio (SNR) when the number of receive antennas N>1. The performance improvement is further enhanced when N or the size of the constellation increases. We relate the problem of ST diversity gain to algebraic number theory, and the coding gain optimization to the theory of simultaneous Diophantine approximation in the geometry of numbers. We find that the coding gain optimization is equivalent to finding irrational numbers "the furthest," from any simultaneous rational approximations.
Quantitative Studies on Plasmalemmal Folds and Caveolae of Rabbit Ventricular Myocardial Cells

Plasmalemmal folds and caveolae were investigated by qualitative and quantitative analysis of electron micrographs obtained by freeze fracture and transmission electron microscopy (TEM) of rabbit right ventricular papillary muscles whose mean sarcomere lengths ranged from 1.64 to 2.28 fun. In passively extended muscles, folds were observed at sarcomere lengths of 2.3 /an and could be shown by extrapolation to become completely extended at a maximum sarcomere length of 2.8 μn. It was concluded that the plasmalemma does not contribute to resting tension in the physiological range of sarcomere lengths. Caveolae are present in both the external plasmalemmal envelope and T-tubular plasmalemma. They show no preferential distribution with respect to underlying myofibrillar striations or membrane folds and are nearly devoid of membrane particles in freeze-fractured material. The surface density of caveolar necks (4.0/pm: apparent plasmalemmal area) is only 16-20% of that reported for frog skeletal muscle. Caveolae augment plasmalemmal area by 21-32%, assuming two or three caveolae per neck, respectively. Caveolar membrane does not serve as a reservoir of membrane to be recruited into external plasmalemma, at least over the physiological range of sarcomere lengths. In heart muscle they do not account for the T-tubular access resistance, and their function in this tissue remains unknown. Circ Res 46: 244-255, 1980
Reexamine the sandhi rules and the merging tones in hakka language

This paper tried to probe the merging tones and the application of sandhi rule for unchecked tones (/24/[33] and /33/[33]) in Hailu variety of Hakka language. Generally speaking, the sandhi rule was applied in both the younger (under 30) and the older (above 50) groups. Tone merging phenomenon (/24/[24] merging toward /33/[33]) was not found in the older group. Yet, the merging phenomenon was found in the younger group. The sandhi rule for /24/ and /33/ was not observed in most of the young speakers. It is proposed that the /24/ and /33/ tones were undergoing sound change by the younger generation.
Attention, Intentions, and the Structure of Discourse

In this paper we explore a new theory of discourse structure that stresses the role of purpose and processing in discourse. In this theory, discourse structure is composed of three separate but interrelated components: the structure of the sequence of utterances (called the linguistic structure), a structure of purposes (called the intentional structure), and the state of focus of attention (called the attentional state). The linguistic structure consists of segments of the discourse into which the utterances naturally aggregate. The intentional structure captures the discourse-relevant purposes, expressed in each of the linguistic segments as well as relationships among them. The attentional state is an abstraction of the focus of attention of the participants as the discourse unfolds. The attentional state, being dynamic, records the objects, properties, and relations that are salient at each point of the discourse. The distinction among these components is essential to provide an adequate explanation of such discourse phenomena as cue phrases, referring expressions, and interruptions.The theory of attention, intention, and aggregation of utterances is illustrated in the paper with a number of example discourses. Various properties of discourse are described, and explanations for the behavior of cue phrases, referring expressions, and interruptions are explored.This theory provides a framework for describing the processing of utterances in a discourse. Discourse processing requires recognizing how the utterances of the discourse aggregate into segments, recognizing the intentions expressed in the discourse and the relationships among intentions, and tracking the discourse through the operation of the mechanisms associated with attentional state. This processing description specifies in these recognition tasks the role of information from the discourse and from the participants' knowledge of the domain.