Miracle-dz/UniFAR-FTUs huggingface dataset:
Lymphokines and Platelets Promote Human Monocyte Adherence to Fibrinogen and Fibronectin In Vitro

Monocytes must accumulate in areas of tissue injury and inflammation to effect phagocytosis, antigen presentation, and monokine production. Fibrinogen/fibronectin matrices have been demonstrated in healing wounds and in delayed‐type hypersensitivity skin reactions. We have developed an in vitro system for investigation of the ability of fibrinogen and fibronectin matrices to serve as substrata for human peripheral blood monocyte adherence. Monocyte adherence was greatest on matrices of both fibrinogen and fibronectin, less to fibrinogen alone, and least to fibronectin alone. Lymphokines increased adherence of monocytes to all three surfaces but not to albumin‐coated surfaces.
Equivalent parameter study of the mechanical properties of super carbon nanotubes

Theoretical studies are made for recent attention-getting super carbon nanotubes. The so-called ‘super carbon nanotube’ is a self-similar structure constructed from low-order carbon nanotubes. Based on the Euler beam theory, the equivalent parameters of super tubes are derived from those of arm tubes, and verified by finite element simulations. Instead of the Young’s modulus E, a new equivalent modulus Eβ is adopted, where β is the ratio of thickness to diameter for arm tubes. The advantage of this equivalent modulus is that the Young’s modulus and thickness do not need to be separated in stiffness calculations. The mechanical properties for composites made of super tubes and matrix are also discussed.
Clustering Oligarchies

We investigate the extent to which clustering algorithms are robust to the addition of a small, potentially adversarial, set of points. Our analysis reveals radical differences in the robustness of popular clustering methods. k-means and several related techniques are robust when data is clusterable, and we provide a quantitative analysis capturing the precise relationship between clusterability and robustness. In contrast, common linkage-based algorithms and several standard objective-function-based clustering methods can be highly sensitive to the addition of a small set of points even when the data is highly clusterable. We call such sets of points oligarchies. Lastly, we show that the behavior with respect to oligarchies of the popular Lloyd’s method changes radically with the initialization technique.
Greater change in bone turnover markers for efavirenz/emtricitabine/tenofovir disoproxil fumarate versus dolutegravir + abacavir/lamivudine in antiretroviral therapy-naive adults over 144 weeks

Objective:Antiretroviral therapy initiation has been linked to bone mineral density and bone biomarker changes. We assessed long-term bone turnover biomarker effects over 144 weeks in patients initiating dolutegravir (DTG) + abacavir/lamivudine (ABC/3TC) versus efavirenz/emtricitabine/tenofovir disoproxil fumarate (EFV/FTC/TDF). Methods:Patients randomized in SINGLE received DTG (50 mg once daily) + ABC/3TC or fixed-dose combination EFV/FTC/TDF. We evaluated vitamin D serum levels and bone turnover markers (BTMs), including type 1 collagen cross-linked C-telopeptide (CTx), osteocalcin, bone-specific alkaline phosphatase (BSAP), and procollagen type 1 N-terminal propeptide (P1NP), at baseline and weeks 48, 96, and 144. Results:Among the 833 enrolled patients (68% white, 85% men), baseline median age was 35 years (range 18–85), median CD4+ was 338 cells/&mgr;l, and median BMI was 24 kg/m2. Fifty-three percent of patients smoked, and 6% reported baseline vitamin D use, with no meaningful differences between groups. Relative to baseline, CTx, osteocalcin, BSAP, and P1NP increased; vitamin D decreased in both groups at weeks 48, 96, and 144. Changes from baseline typically peaked at weeks 48 or 96 and for the four analytes, excluding vitamin D, with the EFV/FTC/TDF group having significantly greater changes from baseline at all time points. Conclusion:DTG + ABC/3TC in antiretroviral therapy-naive patients resulted in significantly lower increases in BTMs (CTx, osteocalcin, BSAP, P1NP) compared with EFV/FTC/TDF over 144 weeks. The observed changes are consistent with results from other smaller, randomized trials. These differences in BTMs likely correlate with changes in bone mineral density over time.
Informant-specific correlates of suicidal behavior in a community survey of 12- to 14-year-olds.

OBJECTIVES To arrive at a better estimation of informant-specific correlates of suicidal behavior in young adolescents and to see how agreements and discrepancies between child and parent informants can contribute to the development of research and interventions. METHOD The weighted sample from the Quebec Child Mental Health Survey conducted in 1992 included 825 adolescents, aged 12 to 14 years, and their parents. The adolescent and one parent were questioned by two different interviewers. The response rate was 80.3%. Three categories of independent variables were assessed: adolescent, family, and socioeconomic characteristics. Logistic regression models were based on the adolescent and parent informant reports. RESULTS Parents identified 6 of the 59 adolescents having reported suicidal ideation and 2 of the 36 adolescents having reported suicide attempts. Two informant-specific models of correlates of suicidal behavior were found. The adolescent model included internalizing and externalizing mental disorders, family stressful events, and parent-adolescent relationship difficulties, while the parent model included perceiving a need for help for the adolescent, parent's depressive disorders, and parent-adolescent relationship difficulties. CONCLUSION The study shows the relevance of considering informant-specific correlates of suicidal behavior in the development of research and interventions targeting youths suicidal behavior.
Identifying the move method refactoring opportunities based on evolutionary algorithm

Evolution is an intrinsic property of real-world software, which is usually accompanied by the degrading in software quality. Software refactoring is regarded as an effective way to improve the design of the code, and many refactoring approaches have been proposed. In this paper, we transform the software refactoring problem as an optimisation problem, and present a simple evolutionary algorithm (EA) to identify the move method refactorings. It uses software networks at the feature (i.e., method and attribute) level, namely SFN, to represent features and their dependencies; it uses an EA to obtain the optimised class structures in SFN. It finally provides a list of methods that should be moved by comparing the optimised class structures with the real class structures. The empirical evaluation of the proposed approach has been performed on one widely known refactoring example, and the feasibility of our approach is illustrated.
Mining frequent bug-fix code changes

Detecting bugs as early as possible plays an important role in ensuring software quality before shipping. We argue that mining previous bug fixes can produce good knowledge about why bugs happen and how they are fixed. In this paper, we mine the change history of 717 open source projects to extract bug-fix patterns. We also manually inspect many of the bugs we found to get insights into the contexts and reasons behind those bugs. For instance, we found out that missing null checks and missing initializations are very recurrent and we believe that they can be automatically detected and fixed.
Control of Acetyl-Coenzyme A Synthetase (AcsA) Activity by Acetylation/Deacetylation without NAD+ Involvement in Bacillus subtilis

ABSTRACT Posttranslational modification is an efficient mechanism for controlling the activity of structural proteins, gene expression regulators, and enzymes in response to rapidly changing physiological conditions. Here we report in vitro and in vivo evidence that the acuABC operon of the gram-positive soil bacterium Bacillus subtilis encodes a protein acetyltransferase (AcuA) and a protein deacetylase (AcuC), which may control the activity of acetyl-coenzyme A (CoA) synthetase (AMP-forming, AcsA) in this bacterium. Results from in vitro experiments using purified proteins show that AcsA is a substrate for the acetyl-CoA-dependent AcuA acetyltransferase. Mass spectrometry analysis of a tryptic digest of acetylated AcsA (AcsAAc) identified residue Lys549 as the sole modification site in the protein. Unlike sirtuins, the AcuC protein did not require NAD+ as cosubstrate to deacetylate AcsAAc. The function of the putative AcuB protein remains unknown.
Robust Laser Speckle Authentication System Through Data Mining Techniques

This paper proposes a speckle image recognition method using data mining techniques to ensure speckle identification system feasible for authentication. This is an interdisciplinary method that integrates the researches of optics, data mining, and image processing. Because objects have unique but imperfect surfaces, their laser speckle is capable of providing suitable identifiable features for authentication. In our method, matching points among speckle images acquired from one plastic card are extracted by scale-invariant feature transform (SIFT). The spatial relations among the matching points are then transformed to 9 direction lower triangular (9DLT) representations. Then, the Apriori algorithm mines frequent patterns so a useful association rule is obtained as the feature to identify the similarity between each of the speckle images for the purpose of authenticity verification. The proposed method is especially robust in the cases of card displacement and luminance change resulted from laser attenuation. Experimental results show that the proposed method has promising results and outperforms existing methods in identification accuracy.
Genetic diversity and insecticide resistance during the growing season in the green peach aphid (Hemiptera: Aphididae) on primary and secondary hosts: a farm-scale study in Central Chile

Abstract The seasonal dynamics of neutral genetic diversity and the insecticide resistance mechanisms of insect pests at the farm scale are still poorly documented. Here this was addressed in the green peach aphid Myzus persicae (Sulzer) (Hemiptera: Aphididae) in Central Chile. Samples were collected from an insecticide sprayed peach (Prunus persica L.) orchard (primary host), and a sweet-pepper (Capsicum annum var. grossum L.) field (secondary host). In addition, aphids from weeds (secondary hosts) growing among these crops were also sampled. Many unique multilocus genotypes were found on peach trees, while secondary hosts were colonized mostly by the six most common genotypes, which were predominantly sensitive to insecticides. In both fields, a small but significant genetic differentiation was found between aphids on the crops vs. their weeds. Within-season comparisons showed genetic differentiation between early and late season samples from peach, as well as for weeds in the peach orchard. The knock-down resistance (kdr) mutation was detected mostly in the heterozygote state, often associated with modified acetylcholinesterase throughout the season for both crops. This mutation was found in high frequency, mainly in the peach orchard. The super-kdr mutation was found in very low frequencies in both crops. This study provides farm-scale evidence that the aphid M. persicae can be composed of slightly different genetic groups between contiguous populations of primary and secondary hosts exhibiting different dynamics of insecticide resistance through the growing season.
The anomalously high transmission into the system "dielectric grating-metal thin film-dielectric grating"

The analysis of the transmission of system "dielectric grating- thin metal film-dielectric grating-substrate" is conducted by method of coupled waves. The 53 diffraction orders are used at the analysis that ensures the suitable precision of numerical calculations. It is reveal, that at the certain parameters the system has the anomalously high transmission for the reflection of about zero. For example, the silver film with thickness of 0.0385 μm, which is placed between a two grating with the certain parameters, transmits more than 0.86 and 0.83 for TE and TM polarizations, respectively, at wave-length of 1.5 μm. Under vacuum the silver film of the same thickness has the reflection more than 0.98 and transmits less than 0.004. The analogical results are obtained for other metals: cold and potassium. The transmittance value sharply decreases at deviation of wavelength from optimum magnitude. Basing on such structures it is possible to build the narrow-banded filters. The effect of great transmission can be explained in the following way. The gratings serve as matched elements of impedance for the thin metal film and of impedance for homogeneous mediums. The field distribution inside structure meets standing wave, node of which placed on thin metal film that leads to low absorption.
Smooth Muscle Cell Deletion of Low-Density Lipoprotein Receptor–Related Protein 1 Augments Angiotensin II–Induced Superior Mesenteric Arterial and Ascending Aortic Aneurysms

Objective—Low-density lipoprotein receptor–related protein 1 (LRP1), a multifunctional protein involved in endocytosis and cell signaling pathways, leads to several vascular pathologies when deleted in vascular smooth muscle cells (SMCs). The purpose of this study was to determine whether LRP1 deletion in SMCs influenced angiotensin II–induced arterial pathologies. Approach and Results—LRP1 protein abundance was equivalent in selected arterial regions, but SMC-specific LRP1 depletion had no effect on abdominal and ascending aortic diameters in young mice. To determine the effects of LRP1 deficiency on angiotensin II vascular responses, SMC-specific LRP1 (smLRP1+/+) and smLRP1-deficient (smLRP1−/−) mice were infused with saline, angiotensin II, or norepinephrine. Several smLRP−/− mice died of superior mesenteric arterial (SMA) rupture during angiotensin II infusion. In surviving mice, angiotensin II profoundly augmented SMA dilation in smLRP1−/− mice. SMA dilation was blood pressure dependent as demonstrated by a similar response during norepinephrine infusion. SMA dilation was also associated with profound macrophage accumulation, but minimal elastin fragmentation. Angiotensin II infusion led to no significant differences in abdominal aorta diameters between smLRP1+/+ and smLRP1−/− mice. In contrast, ascending aortic dilation was exacerbated markedly in angiotensin II–infused smLRP1−/− mice, but norepinephrine had no significant effect on either aortic region. Ascending aortas of smLRP1−/− mice infused with angiotensin II had minimal macrophage accumulation but significantly increased elastin fragmentation and mRNA abundance of several LRP1 ligands including MMP-2 (matrix metalloproteinase-2) and uPA (urokinase plasminogen activator). Conclusions—smLRP1 deficiency had no effect on angiotensin II–induced abdominal aortic aneurysm formation. Conversely, angiotensin II infusion in smLRP1−/− mice exacerbated SMA and ascending aorta dilation. Dilation in these 2 regions had differential association with blood pressure and divergent pathological characteristics.
A Study of Forward Error Correction Schemes for Reliable Transport in Underwater Sensor Networks

Underwater communications is a very challenging topic due to its singular channel characteristics. Most protocols used in terrestrial wireless communications can not be directly applied in the underwater world. A high bit error rate and low propagation delay make the design of reliable transport protocols especially awkward. In this paper, we first propose four schemes that combine forward error correction mechanisms at the bit and/or packet level to increase the reliability in a non-cooperative scenario. The broadcast property of the underwater environment allows us to extend them to a cooperative setting. Based on our analyses, we introduce ADELIN: an adaptive reliable transport protocol for underwater sensor networks. We suggest an architecture for implementation and compare our protocol to other schemes. We show that it succeeds in a better probability and energy tradeoff for both single- and multi-hop communications.
Pitx2 in Embryonic and Adult Myogenesis

Skeletal muscle is a heterogeneous tissue that represents between 30 and 38% of the human body mass and has important functions in the organism, such as maintaining posture, locomotor impulse, or pulmonary ventilation. The genesis of skeletal muscle during embryonic development is a process controlled by an elaborate regulatory network combining the interplay of extrinsic and intrinsic regulatory mechanisms that transform myogenic precursor cells into functional muscle fibers through a finely tuned differentiation program. However, the capacity of generating muscle still remains once these fibers have matured. Adult myogenesis resembles many of the embryonic morphogenetic episodes and depends on the activation of satellite cells that have the potential to differentiate into new muscle fibers. Pitx2 is a member of the bicoid family of homeodomain transcription factors that play an important role in morphogenesis. In the last decade, Pitx2 has emerged as a key element involved in the fine-tuning mechanism that regulates skeletal-muscle development as well as the differentiation and cell fate of satellite cells in adult muscle. Here we present an integrative view of all aspects of embryonic and adult myogenesis in which Pitx2 is involved, from embryonic development to satellite-cell proliferation, fate specification, and differentiation. Those new Pitx2 functions on satellite-cell biology might open new perspectives to develop therapeutic strategies for muscular disorders.
Miniaturized Lumped-Element LTCC Filter With Spurious Spikes Suppressed Vertically-Interdigital-Capacitors

A miniaturized lumped-element 10-layer low temperature co-fired ceramic (LTCC) filter is proposed for the extremely low center-frequency of 60 MHz. The miniaturization is achieved by using spiral inductors with high-impedance lines and spurious spikes suppressed vertically-interdigital-capacitors (SVICs). By interconnecting the open ends of interval fingers with vertical vias, capacitance increment and spurious spikes suppression of vertically-interdigital-capacitor (VIC) are achieved without Q-factor degradation. The proposed filter has the smallest reported size of only 0.004 ×0.004 ×0.0004 λg. Furthermore, comparisons and discussions are also implemented.
Crystal Structure of the Herpesvirus Inner Tegument Protein UL37 Supports Its Essential Role in Control of Viral Trafficking

ABSTRACT In cells infected with herpesviruses, two capsid-associated, or inner tegument, proteins, UL37 and UL36, control cytosolic trafficking of capsids by as yet poorly understood mechanisms. Here, we report the crystal structure of the N-terminal half of UL37 from pseudorabies virus, an alphaherpesvirus closely related to herpes simplex viruses and varicella-zoster virus. The structure—the first for any alphaherpesvirus inner tegument protein—reveals an elongated molecule of a complex architecture rich in helical bundles. To explore the function of the UL37 N terminus, we used the three-dimensional framework provided by the structure in combination with evolutionary trace analysis to pinpoint several surface-exposed regions of potential functional importance and test their importance using mutagenesis. This approach identified a novel functional region important for cell-cell spread. These results suggest a novel role for UL37 in intracellular virus trafficking that promotes spread of viral infection, a finding that expands the repertoire of UL37 functions. Supporting this, the N terminus of UL37 shares structural similarity with cellular multisubunit tethering complexes (MTCs), which control vesicular trafficking in eukaryotic cells by tethering transport vesicles to their destination membranes. Our results suggest that UL37 could be the first viral MTC mimic and provide a structural rationale for the importance of UL37 for viral trafficking. We propose that herpesviruses may have co-opted the MTC functionality of UL37 to bring capsids to cytoplasmic budding destinations and further on to cell junctions for spread to nearby cells. IMPORTANCE To move within an infected cell, viruses encode genes for proteins that interact with host trafficking machinery. In cells infected with herpesviruses, two capsid-associated proteins control the cytosolic movement of capsids by as yet poorly understood mechanisms. Here, we report the crystal structure for the N-terminal half of one of these proteins, UL37. Structure-based mutagenesis revealed a novel function for UL37 in virus trafficking to cell junctions for cell-cell spread. The unexpected structural similarity to components of cellular multisubunit tethering complexes, which control vesicular traffic, suggests that UL37 could be the first viral MTC mimic and provides a structural basis for the importance of UL37 for virus trafficking.
Min-Max Relations for Odd Cycles in Planar Graphs

Let $\nu(G)$ be the maximum number of vertex-disjoint odd cycles of a graph $G$ and $\tau(G)$ the minimum number of vertices whose removal makes $G$ bipartite. We show that $\tau(G)\le 6\nu(G)$ if $G$ is planar. This improves the previous bound $\tau(G)\le 10\nu(G)$ by Fiorini et al. [Math. Program. Ser. B, 110 (2007), pp. 71--91].
Meaning Text theory and dependency tree semantics: an account of underspecification

This paper presents an approach to semantic interpretation for MTT that accounts for ambiguities of quantifier scoping. Dependency Tree Semantics (DTS) is described as a target formalism that introduces in the SemS a mechanism for dealing with quantifiers. DTS is based on underspecification, i.e. all ambiguous interpretations of a quantified sentence are represented in a single structure, where the scope relations are not given. The underspecified representations can be extended by adding dependency arcs that express the scope ordering when enough information is available for the disambiguation. Since a single underspecified structure covers all readings of a sentence, the mapping from the SSyntS to the SemS is heavily simplified. In order to provide some evidence about this, the paper includes the definition of the syntax-semantics mapping for a small fragment of English.
Performance analysis of direct position determination for emitter source positioning

Wireless communication systems are becoming very popular and playing a vital role in people's daily life. Location based services are attracting more and more attention by service providers as well as by researchers. Such traditional location methods as Time of Arrival (TOA) and Angle of Arrival (AOA) [1] are widely used in emitter localization and vehicle navigations. These methods are two-step location methods measuring a single time or angle parameter first and then determine emitter locations. Recently, a new one-step location method, called Direct Position Determination (DPD), has been proposed by Anthony J. Weiss in [2] for its high positioning accuracy and advantages over traditional location techniques.
Estimating target signatures with diverse density

Hyperspectral target detection algorithms rely on knowing the desired target signature in advance. However, obtaining an effective target signature can be difficult; signatures obtained from laboratory measurements or hand-spectrometers in the field may not transfer to airborne imagery effectively. One approach to dealing with this difficulty is to learn an effective target signature from training data. An approach for learning target signatures from training data is presented. The proposed approach addresses uncertainty and imprecision in groundtruth in the training data using a multiple instance learning, diverse density (DD) based objective function. After learning the target signature given data with uncertain and imprecise groundtruth, target detection can be applied on test data. Results are shown on simulated and real data.