Miracle-dz/UniFAR-FTUs huggingface dataset:
Exploring Abbreviation Expansion for Genomic Information Retrieval

Abbreviations are commonly found instances of synonymy in Biomedical journal papers. Information retrieval systems that index paragraphs rather than full-text articles are more susceptible to term variation of this kind, since abbreviations are typically only defined once at the beginning of the text. One solution to this problem is to expand the user query automatically with all possible abbreviation instances for each query term. In this paper, we compare the effectiveness of two abbreviation expansion techniques on the TREC 2006 Genomics Track queries and collection. Our results show that for highly ambiguous abbreviations the query collocationeffect isn’t strong enough to deter the retrieval of erroneous passages. We conclude that full-text abbreviation resolution prior to passage indexing is the most appropriate approach to this problem.
The ci/bH moiety in the b6f complex studied by EPR: A pair of strongly interacting hemes

X-band EPR features in the region of 90–150 mT have previously been attributed to heme ci of the b6 complex [Zhang H, Primak A, Bowman MK, Kramer DM, Cramer WA (2004) Biochemistry 43:16329–16336] and interpreted as arising from a high-spin species. However, the complexity of the observed spectrum is rather untypical for high-spin hemes. In this work, we show that addition of the inhibitor 2-n-nonyl-4-hydroxyquinoline N-oxide largely simplifies heme ci's EPR properties. The spectrum in the presence of 2-n-nonyl-4-hydroxyquinoline N-oxide is demonstrated to be caused by a simple S = 5/2, rhombic species split by magnetic dipolar interaction (Axx = 7.5 mT) with neighboring heme bH. The large spacing of lines in the uninhibited system, by contrast, cannot be rationalized solely on the basis of magnetic dipolar coupling but is likely to encompass strong contributions from exchange interactions. The role of the H2O/OH− molecule bridging heme ci's Fe atom and heme bH's propionate side chain in mediating these interactions is discussed.
Functional Manipulation of a Calcium-binding Protein from Entamoeba histolytica Guided by Paramagnetic NMR*

Background: EhCaBP1 is one of the EF-hand calcium-binding proteins (CaBP) involved in various Ca2+ signaling pathways. Results: Hydrophobic residues at the −4 position of the Ca2+-binding loop affects structure, Ca2+-binding properties, and cellular localization of EhCaBP1. Conclusion: The Y81F mutation in EhCaBP1 makes it more structured like CaM and TnC. Significance: Observed variations in the structures and cellular localization of the wt and mutant could have influence on their biological behavior. EhCaBP1, one of the calcium-binding proteins from Entamoeba histolytica, is a two-domain EF-hand protein. The two domains of EhCaBP1 are structurally and functionally different from each other. However, both domains are required for structural stability and a full range of functional diversity. Analysis of sequence and structure of EhCaBP1 and other CaBPs indicates that the C-terminal domain of EhCaBP1 possesses a unique structure compared with other family members. This had been attributed to the absence of a Phe-Phe interaction between highly conserved Phe residues at the −4 position in EF-hand III (F[-4]; Tyr81) and at the 13th position in EF-hand IV (F[+13]; Phe129) of the C-terminal domain. Against this backdrop, we mutated the Tyr residue at the −4th position of EF III to the Phe residue (Y81F), to bring in the Phe-Phe interaction and understand the nature of structural and functional changes in the protein by NMR spectroscopy, molecular dynamics (MD) simulation, isothermal titration calorimetry (ITC), and biological assays, such as imaging and actin binding. The Y81F mutation in EhCaBP1 resulted in a more compact structure for the C-terminal domain of the mutant as in the case of calmodulin and troponin C. The compact structure is favored by the presence of a π-π interaction between Phe81 and Phe129 along with several hydrophobic interactions of Phe81, which are not seen in the wild-type protein. Furthermore, the biological assays reveal preferential membrane localization of the mutant, loss of its colocalization with actin in the phagocytic cups, whereas retaining its ability to bind G- and F-actin.
An Optical Method of Strain Measurement in the Split Hopkinson Pressure Bar

With the recent advancements in laser technology, the use of the laser as a measurement tool has become more widespread. Currently, research is underway in which a semiconductor laser diode is being used to measure the radial strain of a plastically deforming test specimen at the Naval Surface Warfare Center Dahlgren Division (NSWCDD). This particular application involves the use of a 670 nanometer (mm) wavelength laser diode and 25 megahenz (MHz) optical detector in lieu of conventional electrical resistance strain gages to measure specimen true strain in the split Hopkinson pressure bar (SHPB), a compressive stress testing apparatus capable of generating strain rates up to IO4 s-‘. Preliminary data has shown that, for incompressible materials, this optical method of strain measurement results in increased resolution, bandwidth and sIgnal-to-noise ratios such that identification of both the elastic and plastic deformation regimes is possible. In addition, peak specimen strains and strain rates can be resolved Finally, this study will show that the use of the optical method of strain measurement improves the precision of the SHPB experiment by rldding the expernnent of the errors associated with the elecmcal resistance stram gage.
Regionally specific alterations in functional connectivity of the anterior cingulate cortex in major depressive disorder

Background Depression has been associated with functional alterations in several areas of the cingulate cortex. In this study we have taken a systematic approach to examining how alterations in functional connectivity vary across the functionally diverse subregions of the rostral cingulate cortex. Method Eighteen patients with major depressive disorder, aged 15 to 24 years, were matched with 20 healthy control participants. Using resting-state functional connectivity magnetic resonance imaging (fcMRI), we systematically investigated the functional connectivity of four subregions of the rostral cingulate cortex. Voxelwise statistical maps of each subregion's connectivity with other brain areas were compared between the patient and control groups. Results The depressed participants showed altered patterns of connectivity with ventral cingulate subregions. They showed increased connectivity between subgenual anterior cingulate cortex (ACC) and dorsomedial frontal cortex, with connectivity strength showing positive correlation with illness severity. Depressed participants also showed increased connectivity between pregenual ACC and left dorsolateral frontal cortex, and decreased connectivity between pregenual ACC and the caudate nucleus bilaterally. Conclusions The results reinforce the importance of subgenual ACC for depression, and show a close link between brain regions that support self-related processes and affective visceromotor function. The pregenual ACC also has an important role, with its increased connectivity with dorsolateral frontal cortex suggesting heightened cognitive regulation of affect; and reduced connectivity with the caudate nucleus potentially underlying symptoms such as anhedonia, reduced motivation and psychomotor dysfunction.
Genetic Characterization of Trypanosoma cruzi DTUs in Wild Triatoma infestans from Bolivia: Predominance of TcI

Background The current persistence of Triatoma infestans (one of the main vectors of Chagas disease) in some domestic areas could be related to re-colonization by wild populations which are increasingly reported. However, the infection rate and the genetic characterization of the Trypanosoma cruzi strains infecting these populations are very limited. Methodology/Principal Findings Of 333 wild Triatoma infestans specimens collected from north to south of a Chagas disease endemic area in Bolivia, we characterized 234 stocks of Trypanosoma cruzi using mini-exon multiplex PCR (MMPCR) and sequencing the glucose phosphate isomerase (Gpi) gene. Of the six genetic lineages (“discrete typing units”; DTU) (TcI-VI) presently recognized in T. cruzi, TcI (99.1%) was overdominant on TcIII (0.9%) in wild Andean T. infestans, which presented a 71.7% infection rate as evaluated by microscopy. In the lowlands (Bolivian Chaco), 17 “dark morph” T. infestans were analyzed. None of them were positive for parasites after microscopic examination, although one TcI stock and one TcII stock were identified using MMPCR and sequencing. Conclusions/Significance By exploring large-scale DTUs that infect the wild populations of T. infestans, this study opens the discussion on the origin of TcI and TcV DTUs that are predominant in domestic Bolivian cycles.
A Research on the Internal Control Information’s Disclosure of Signal Game Model of the Listed Companies

This paper studied the game theory about that the listed companies used internal control disclosure as signal under the condition of incomplete information, constructed a signal game model to analyze the internal control information disclosure problem under the condition of incomplete information. It also proposed some policy Suggestions to inspire the listed companies to disclose internal control message veritably.
Coexisting middle ear cholesteatoma and giant petrous apex cholesterol granuloma.

*Department of OtolaryngologyYHead and Neck Surgery, Bnai Zion Medical Center, Technion-Israel Institute of Technology, Haifa; ÞDepartment of Radiology, Tel-Aviv Sourasky Medical Center, Tel-Aviv University, Tel-Aviv; þDepartment of OtolaryngologyYHead and Neck Surgery, Carmel Medical Center, Technion-Israel Institute of Technology, Haifa, Israel; and §Department of OtolaryngologyYHead and Neck Surgery, and Neurological Surgery, University of Southern California School of Medicine, House Ear Clinic, Los Angeles, California, U.S.A.
Proteasomal Turnover of Hepatitis C Virus Core Protein Is Regulated by Two Distinct Mechanisms: a Ubiquitin-Dependent Mechanism and a Ubiquitin-Independent but PA28γ-Dependent Mechanism

ABSTRACT We have previously reported on the ubiquitylation and degradation of hepatitis C virus core protein. Here we demonstrate that proteasomal degradation of the core protein is mediated by two distinct mechanisms. One leads to polyubiquitylation, in which lysine residues in the N-terminal region are preferential ubiquitylation sites. The other is independent of the presence of ubiquitin. Gain- and loss-of-function analyses using lysineless mutants substantiate the hypothesis that the proteasome activator PA28γ, a binding partner of the core, is involved in the ubiquitin-independent degradation of the core protein. Our results suggest that turnover of this multifunctional viral protein can be tightly controlled via dual ubiquitin-dependent and -independent proteasomal pathways.
RF mixers using standard digital CMOS 0.35 /spl mu/m process

The performance of doubly-balanced active and resistive RF CMOS mixers is presented following measurements at 1.8-GHz RF frequency. The active mixer has demonstrated 10.4-dB gain, 7-dB SSB NF, -6 dBm IIP3 and consumes 9.7 mA under 3 V. The passive mixer has demonstrated 7.5-dB loss, 10-dB SSB NF and +16-dBm of input IP3.
Attribute Series of Software Evolution for Software Quality Assessment

The Varity and complexity of software increased from day to day, the software quality assurance must be used to make a balance between quality and productivity. In software applications defect density and defect prediction are essential for efficient resource allocation in software evolution. We presented a new approach to software defect prediction based on value series of evolution attributes. In an empirical study we applied data mining techniques for value series based on evolution attributes. For that, we developed models utilizing genetic programming and linear regression to accurately predict software defects. In our study, we investigated the data of three independent projects, two open source and one commercial software system. The results show that by utilizing series of these attributes we obtain models with high correlation coefficients (between 0.716 and 0.946). Further, we argue that prediction models based on series of a single variable are sometimes superior to the model including all attributes: in contrast to other studies that resulted in size or complexity measures as predictors, we have identified the number of authors and the number of commit messages to versioning systems as excellent predictors of defect densities. Keywords— Defect Density, Quality Assessment, Data mining
What Makes a Good Review: Analyzing Reviews on JD.com

Reviews are contents written by users to express opinions on products or services. However, the number of reviews is always large and the quality of reviews is various. In order to assess the quality of reviews, we ought to know the factors that have influence on or are related to the quality of reviews. In this paper, we present an in-depth study of reviews on JD.com, one of the famous E-commerce sites in China. We observed the times when users buy goods are highly related to the time when they post reviews. Meanwhile, the level of users is an important factor affects the quality of reviews. On the other hand, users prefer to post short reviews containing the description of the quality and price of the product. Based on a lexical resource containing sentiment annotations, we found sentimental words expressing users' feelings and opinions is one of the key factors that can influence the quality of reviews. Finally, we evaluated the importance of more than 18 factors influencing the quality of reviews, and found these factors can be compressed into 5 principal factors.
Dense Image Registration and Deformable Surface Reconstruction in Presence of Occlusions and Minimal Texture

Deformable surface tracking from monocular images is well-known to be under-constrained. Occlusions often make the task even more challenging, and can result in failure if the surface is not sufficiently textured. In this work, we explicitly address the problem of 3D reconstruction of poorly textured, occluded surfaces, proposing a framework based on a template-matching approach that scales dense robust features by a relevancy score. Our approach is extensively compared to current methods employing both local feature matching and dense template alignment. We test on standard datasets as well as on a new dataset (that will be made publicly available) of a sparsely textured, occluded surface. Our framework achieves state-of-the-art results for both well and poorly textured, occluded surfaces.
Performance evaluation of e-Business in Australia

The Internet and related technologies have made a substantial impact on the way organisations conduct business in Australia and around the world. Australian organisations like their international counterparts have invested heavily to leverage the Internet and transform their traditional businesses into e-businesses in the last seven years. E-business investments are claiming a sizeable share of overall IT budgets in most organisations whether they are small, medium or large. However, managers are under constant pressure to justify e-business costs and to ensure that these investments keep paying off. Earlier research on e-business in Australia addressed issues of the rate of e-business uptake and the application of the Internet to certain business processes. Research discussed in this paper is one of the first attempts to evaluate the value of e-business. It is based on data collected, collated and analysed from the responses received from IT and e-business managers throughout Australia. Research presented in this paper is based on a model developed in the USA (Barua et al, 2001) to identify the impact of e-business drivers on operational excellence of firms which influence financial improvements. It was initiated to quantify the success of e-business in Australia after huge losses from e-business projects were reported by a few large organisations. The paper includes a review of literature on e-business evaluation, research methodology, analysis techniques, a discussion of e-business performance in Australia and presents the impact of e-business on operational excellence and financial performance of the organisation.
Optic Neuritis and Retinal Ganglion Cell Loss in a Chronic Murine Model of Multiple Sclerosis

Multiple sclerosis (MS) and its animal model experimental autoimmune encephalomyelitis (EAE) are neurodegenerative diseases with characteristic inflammatory demyelination in the central nervous system, including the optic nerve. Neuronal and axonal damage is considered to be the main cause of long-term disability in patients with MS. Neuronal loss, including retinal ganglion cell (RGC) apoptosis in eyes with optic neuritis (ON), also occurs in EAE. However, there is significant variability in the clinical course and level of neuronal damage in MS and EAE. The current studies examine the mechanisms and kinetics of RGC loss in C57/BL6 mice immunized with myelin oligodendrocyte glycoprotein to induce a chronic EAE disease. Clinical progression of EAE was scored daily and vision was assessed by optokinetic responses. At various time points, RGCs were counted and optic nerves were examined for inflammatory cell infiltration. Almost all EAE mice develop ON by day 15 post-immunization; however, RGC loss is delayed in these mice. No RGC loss is detected 25 days post-immunization, whereas RGC numbers in EAE mice significantly and progressively decrease compared to controls from 35 to 50 days post-immunization. The delayed time course of RGC loss is in stark contrast to that reported in relapsing EAE, as well as in rats with chronic EAE. Results suggest that different clinical disease courses of optic nerve inflammation may trigger distinct mechanisms of neuronal damage, or RGCs in different rodent strains may have variable resistance to neuronal degeneration.
Thiazolidinedione drugs in the treatment of type 2 diabetes mellitus: past, present and future

Abstract Thiazolidinedione (TZD) drugs used in the treatment of type 2 diabetes mellitus (T2DM) have proven effective in improving insulin sensitivity, hyperglycemia, and lipid metabolism. Though well tolerated by some patients, their mechanism of action as ligands of peroxisome proliferator-activated receptors (PPARs) results in the activation of several pathways in addition to those responsible for glycemic control and lipid homeostasis. These pathways, which include those related to inflammation, bone formation, and cell proliferation, may lead to adverse health outcomes. As treatment with TZDs has been associated with adverse hepatic, cardiovascular, osteological, and carcinogenic events in some studies, the role of TZDs in the treatment of T2DM continues to be debated. At the same time, new therapeutic roles for TZDs are being investigated, with new forms and isoforms currently in the pre-clinical phase for use in the prevention and treatment of some cancers, inflammatory diseases, and other conditions. The aims of this review are to provide an overview of the mechanism(s) of action of TZDs, a review of their safety for use in the treatment of T2DM, and a perspective on their current and future therapeutic roles.
Expectation Maximization for Combined Phylogenetic and Hidden Markov Models Adam Siepel December

An expectation maximization (EM) algorithm is derived to estimate the parameters of a phylogenetic model, a probabilistic model of molecular evolution that considers the phylogeny, or evolutionary tree, by which a set of present-day organisms are related. The EM algorithm is then extended for use with a combined phylogenetic and hidden Markov model. An efficient method is also shown for computing gradients of the log likelihood of a phylogenetic model, which is similar in spirit to the EM algorithms, but has applications beyond EM—for example, in improving the efficiency of the quasi-Newton or conjugategradient methods that are commonly used to fit phylogenetic models. Finally, a small set of experiments are discussed in which the time to fit a phylogenetic model is compared among the EM algorithm, a standard quasi-Newton algorithm, and a modified quasi-Newton algorithm that computes gradients in the new, more efficient way. The performance of all algorithms is compared with that of PAML, a widely used software package for phylogenetic modeling. The modified quasi-Newton and EM algorithms both improve considerably on the standard quasi-Newton algorithm, and are competitive with PAML, despite that little care has been given to performance tuning. The EM algorithm seems particularly promising, despite somewhat slow convergence and a tendency occasionally to become “stuck” for several iterations at suboptimal parameter values. These problems may be addressed by the “entropic update” of Singer and Warmuth, which remains to be implemented and tested.
Inhibitory Activity of Myelin-Associated Glycoprotein on Sensory Neurons Is Largely Independent of NgR1 and NgR2 and Resides within Ig-Like Domains 4 and 5

Myelin-associated glycoprotein (MAG) is a sialic acid binding Ig-like lectin (Siglec) which has been characterized as potent myelin-derived inhibitor of neurite outgrowth. Two members of the Nogo-receptor (NgR) family, NgR1 and NgR2, have been identified as neuronal binding proteins of MAG. In addition, gangliosides have been proposed to bind to and confer the inhibitory activity of MAG on neurons. In this study, we investigated the individual contribution of NgRs and gangliosides to MAG-mediated inhibition of sensory neurons derived from dorsal root ganglia (DRG) of ngr1, ngr2 or ngr1/ngr2 deletion mutants. We found no disinhibition of neurite growth in the absence of either NgR1 or NgR2. Sensory neurons deficient for both NgR proteins displayed only a moderate reduction of MAG-mediated inhibition of neurite growth. If treated with Vibrio cholerae neuraminidase (VCN), inhibition by MAG is further attenuated but still not annulled. Thus, disrupting all known protein and ganglioside receptors for MAG in sensory neurons does not fully abolish its inhibitory activity pointing to the existence of as yet unidentified receptors for MAG. Moreover, by employing a variety of protein mutants, we identified the Ig-like domains 4 or 5 of MAG as necessary and sufficient for growth arrest, whereas abolishing MAG's ability to bind to sialic acid did not interfere with its inhibitory activity. These findings provide new insights into the inhibitory function of MAG and suggest similarities but also major differences in MAG inhibition between sensory and central nervous system (CNS) neurons.
Recovery Nutrition: Timing and Composition after Endurance Exercise

Consumption of macronutrients, particularly carbohydrate (CHO) and possibly a small amount of protein, in the early recovery phase after endurance exercise can enhance muscle glycogen resynthesis rates. A target of at least 1.2 g·kg body weight−1·h−1 CHO (over several hours) is suggested. This rate of CHO intake could be sustained with liquid, gel, or solid food rich in CHO for maximizing muscle glycogen. Whether the coingestion of protein with CHO compared with isocaloric CHO results in meaningful differences in glycogen replenishment that translate into subsequent performance enhancement is equivocal. Advantages of added protein with CHO in reducing true muscle damage from endurance exercise remain to be verified. There are, however, no apparent contraindications for using milk or specialty CHO/protein/amino acid products either. Future investigations that examine signaling mechanisms within muscle should be conducted in parallel with translational evidence in humans.